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This section covers the instructions for submitting a new IACUC protocol. For information on how to submit an amendment, complete an annual review, or complete a third year renewal please see the other help pages.

There are many considerations that need to be taken to write an IACUC protocol. Below are instructions to complete each section of the protocol. Contained with each section are the purpose, regulatory requirements (why the section or question is required), followed by detailed instructions for what the IACUC is looking for during review. If you have any questions or need clarification, please contact the IACUC office for help.

This page can be considered to be a “staging” page that determines which pages related to each species that you are working with will be available for adding information. For example, if you are performing non-surgical procedures on the species, please select “Yes” to that question. Section 5.11 will then be available for you to add details about the non-surgical procedures that you are proposing. Please go through each question carefully so that you can ensure that the information required for the particular species can be provided later in the protocol.

Lay Summary: The primary aim of the lay summary is to describe your work to the non-scientific world.

Regulatory Requirement: The IACUC is comprised of educated lay members of varied scientific backgrounds, members of the scientific community from a variety of disciplines, as well as professionals in the areas of animal housing and care. A "lay summary" is required for the Committee to determine if the protocol meets U.S. Government Principle II "Procedures involving animals should be designed and performed with due consideration for relevance to human or animal heath, the advancement of knowledge, or the good of society."

What the IACUC expects: (250 words or less)

  • Briefly describe the major goals of the research and why the animal model you chose is the appropriate model.
  • Write in non-technical language. All abbreviations/acronyms should be defined on first use. For example, how would you describe your work to a group of high school students?
  • Be clear and concise; several sentences to one or two short paragraphs of 250 words or less, should be adequate.



Scientific Design: Provide scientific justification for your experimental design, focusing on the use and need for animals to achieve your goals. For instructional protocols describe the exercises which involve the use of animals, and how this relates to the goals of the courses (attach a course syllabus for every course covered in the protocol). The purpose of this section is to enable the committee to evaluate how the proposed work or activity affects animal welfare, and whether the use of animals is appropriately justified. Details of post mortem procedures are not required and should not be provided. Please do not simply attach a copy of your grant proposal!

What the IACUC expects: This section is supposed to be an overview of the entire protocol, including non-surgical and surgical procedures. Specifics on each of these aspects will be described in subsequent sections of the protocol.

  • An overview of each scientific approach that you intend to use describing treatment groups and time intervals 
  • The scientific purpose(s) and justification for using the animals of each species.
  • All non-surgical and surgical procedures to be used on live animals.

Purpose: To justify that the species you propose using is the best species for these studies.

What the IACUC expects: (100 words or less)

  • In general the species requested should be the best suited to the goals of the protocol. Non-animal and invertebrate models should be considered.
  • Acceptable justification may be based on:
    • Species specific genetic characteristics or reagent availability.
    • Required size
    • Building upon existing data bases
    • Unique biological characteristics
  • Examples:
    • "20 years of studies have utilized the rabbit; rather than perform pilot studies to assess murine utility for these studies we propose to continue this research in rabbits."
    • "Training for laparoscopy requires an animal of approximately human dimensions."
    • "apoE knockout constructs are generally available only in mice and many immunologic agents are only available for mouse tissues."

Purpose: To assure that animals come from approved venders or other sources with an acceptable health history, both to protect existing animals in Cornell facilities and to comply with requirements of the Animal Welfare Act and Animal Welfare regulations.

What the IACUC expects: (50 words or less)

  • List the vendors.
  • If coming from another protocol provide the protocol number.
  • If coming from another institution, verify the accreditation status (AAALAC or US PHS Assurance). Be prepared to help make arrangements for transfer of animal health records.
  • If privately-owned, be sure to attach an Owner Consent Form.

Purpose: To describe the order of procedures to be performed on live animals, so the IACUC can evaluate the impact on the animals, as related to animal welfare.

What the IACUC expects: (250 words or less)

  • Provide a timeline and/or a sequential list of all procedures (e.g. blood collection, surgery, behavioral training, administration of substances or test compounds, breeding, tumor induction, etc.) to be performed on all live animals.
  • Details of procedures will be requested in subsequent sections and should not be incorporated here.
  • Do not describe in vitro procedures performed on tissues after removal from animals.

Purpose: To provide a detailed description of any procedures which will be performed on live animals not described under Surgery, Restraint, or Euthanasia.


  • Non-surgical procedure: Any procedure performed on a live animal that does not meet the definitions below of surgery, restraint, or euthanasia.
  • Major surgery: Surgery which penetrates and exposes any body cavity, including the cranium and the perineum, involves orthopedic surgery, or produces significant impairment of anatomic or physiologic function.
  • Minor surgery: Surgery which does not expose a body cavity and causes little or no anatomic or physiologic impairment.
  • Restraint: Physical (manual or mechanical) or chemical (anesthetic or tranquilizer not used in conjunction with surgery) means to limit some or all of an animal’s normal movement or behavior.
  • Euthanasia: The humane destruction of an animal accomplished by a method that produces rapid unconsciousness and subsequent death without evidence of pain or distress, or a method that utilizes anesthesia produced by an agent that causes painless loss of consciousness and subsequent death.

Surgical procedures should be listed and described in 5.12 Surgical Procedures. Describe physical or chemical restraint in 5.9 Restraint Types. Euthanasia procedures are described in 5.16 Euthanasia Method Information.

Purpose: To provide a detailed description of the surgical procedure(s) which will be performed on animals.


  • Major surgery: Surgery which penetrates and exposes a body cavity, produces substantial impairment of physical or physiologic function, or involves extensive tissue dissection or transection. The IACUC will determine whether a surgery is "major" or "minor" on a case-by-case basis, particularly regarding laparoscopic surgery. An important consideration in the determination is the potential for pain and post-op complications.
  • Minor surgery: Surgery which does not expose a body cavity and causes little or no anatomic or physiologic impairment.
  • Survival surgery: The animal awakens from surgical anesthesia.
  • Non-survival surgery: The animal is euthanized before recovery from anesthesia.
  • Restraint: Physical (manual or mechanical) or chemical (anesthetic or tranquilizer not used in conjunction with surgery) means to limit some or all of an animal’s normal movement or behavior.
  • Non-surgical procedure: Any procedure preformed on a live animal that does not meet the above definitions of surgery, restraint or euthanasia.

Procedures not meeting the definition of surgery should be listed and described in 5.11 Non-Surgical Procedures, or in 5.9 Restraint Types.

What the IACUC expects: (250 words or less in descriptive subsections) Provide details of what will be done in the various subsections. Consult a CARE Veterinarian for assistance in completing this information if needed.

  • Surgery:
    • Type of surgery to be performed: Select from the drop-down list or type in space provided.
    • Survival/Non-survival Surgery? Answers to both questions are required. Note that the same surgical procedure could be survival for some animals and non-survival for others, or if performed more than once on a given animal could be survival the first time and non-survival the last time.
  • Pre-Op Procedures and Anesthesia:
    • Identify the ACUP being used as a pre-operative guide: Select from the ACUP list but also provide concise descriptions of key aspects under the protocol sections below.
    • Describe pre-op procedures.
    • Describe surgical site preparation.
    • List who will perform, or supervise anesthesia, and describe their qualifications. If anesthesia service will be provided by CUHA or CARE, reference ACUP 806. In this case anesthetic drugs do not need to be listed in Section 5.15 Administered Substances.
    • If a neuromuscular blocking agent will be used, please justify, and describe how anesthesia levels will be monitored. Note that use of neuromuscular blocking agents is discouraged. If you intend to use one, provide extra detail in this section.
    • How will anesthesia depth be measured? Examples: toe-pinch response, palpebral response, heart rate, respiration rate, blood pressure (BP) monitoring, electrocardiogram, arterial blood gas measurement, alveolar gas measurement (ETCO2), etc.
    • Maximum duration of anesthesia.
  • Surgical Care:
    • Identify ACUP being used as a guide for the surgery procedure: Select from the ACUP list but also provide concise descriptions of key aspects under the protocol sections below.
    • List who will perform or supervise surgery and describe their qualifications.
    • Describe surgical procedure.
    • Give average duration of surgery.
    • Describe surgery incision closure.
  • Post-Op Care:
    • Identify ACUP(s) being used as guides for Post Operative Care: Select from the ACUP list but also provide concise descriptions of key aspects under the protocol sections below.
    • Describe postoperative care. Include specifics on: the frequency of observation; the agent(s) administered, identity of the responsible individual(s); and the detection and management of postoperative complications during work hours, weekends, and holidays. The ACUP plus the specific information provided here should allow a skilled, trained individual to step in and perform the postoperative care exactly as it is intended under this protocol.
    • If sutures or staples must be removed, specify the time-limit post-surgery.

Purpose: Multiple major survival surgery is defined as more than one major operative procedure from which the animal is allowed to recover.

There is no need to justify separately procedures that involve one major survival surgery and one major terminal surgery.


  • Major surgery: Surgery which penetrates and exposes any body cavity, including the cranium and the peritoneum, involves orthopedic surgery, or produces significant impairment of anatomic or physiologic function.
  • Multiple major survival surgery: more than one major operative procedure from which the animal is allowed to recover

What the IACUC expects: (250 words or less)
Performance of more than one major survival surgery on a single animal is discouraged but may be approved by the IACUC if scientifically justified by the investigator.

  • Some examples of valid justifications are: 
    • If it is a necessary, related component of one integrated research approach.
    • Conserves scarce animal resources.
    • If it is required for veterinary care reasons, e.g, animal health.

Purpose: Provide evidence that you have thought through how many animals you will need and will be using the minimal number of animals necessary.

This is the page where you also enter the total number of animals requested for the three years of the protocol approval period. Please note that the total number of animals requested is not for one year, but for the entire duration of the three-year protocol. This number must be justified in the Justification for Number of Animals portion of Section 5.17 and must account for all the animals per pain category.  Usually, yearly numbers multiplied by number of years equals the protocol total. For example, if a course uses 10 animals each year and the course will be held for three years, then the total number of animals that must be requested and justified, is 30.

In some cases, though, the number of animals used per year is the total number requested for the three-year duration. For example: a dog protocol uses 10 animals per year. The same 10 animals will be used for three years. In this case, the number for protocol total and the yearly number would be the same, i.e., 10. In the Justification for Number of Animals, the PI must clearly state this to avoid confusion.

What the IACUC expects: (50 to 1,000 words depending on complexity)

In all cases, a rational basis for the number of animals requested must be provided. If several studies of different design are planned as part of your protocol, provide a justification of numbers of animals for each study type.

Detail the basis for the specific number of animals you propose using.

  • If you are testing a hypothesis (e.g., plan to report a p-value with your results) or are comparing two or more groups of animals, the number of animals must be justified statistically with a power analysis. You must also justify the number of groups in each study and the need for repeated studies, besides justifying the number of animals per group. 


Guidance for Statistical Justification of Numbers:

Individual animals treated in the same manner often show variation in the measured variable. Moreover, a greater variation impedes discovery of a small, but real, difference. We are required to judge whether the numbers of animals you are proposing are statistically justified.

Statistical tests provide a way to estimate whether the differences measured between groups of animals treated differently in one experiment are "real" (will be reproducible nearly all the time), or whether they just occurred by chance. Most often this is stated as the p-value. (p < 0.05 means the "result" could occur just by chance less than 5% of the time). From simple t-Tests to the most complicated analyses, the mathematical assumptions underlying statistical tests also require that the methods of analysis, the p-value, and the minimal difference between groups you want to find, all be decided upon beforehand.

The IACUC expects that you will describe the statistical test(s) you will use (and be prepared to defend) and provide information on the following:

  • The p-value you set for a statistically significant result. This value is also often known as the alpha significance level (or probability).
  • The variation between animals treated the same way. The variance is often expressed as sigma, the sample standard deviation (statistical way of expressing the precision of the observed measures within a group of animals treated the same way).
  • The minimal effect size (difference in the measures between groups) you are looking for, the size of difference that you would consider to be biologically meaningful and worth interpreting.
  • The statistical power you are aiming to achieve. Power is one minus beta (the probability of failing to reject the null hypothesis when it is actually false), and most researchers rather arbitrarily accept powers of 0.8.
  • The minimal number of animals per group needed to find the minimal effect size from a power analysis appropriate to your statistical test using the above information.
  • You must also justify the number of groups (different treatments, levels of treatment, etc.) in each study. If for any reason you are replicating studies, you will also need to explicitly justify the need for repeated studies.

If you are unsure what to do, or have a complicated or rare experimental design, consult a statistical service unit (e.g. Cornell statistical consulting unit), or a statistician.

Cornell's IACUC does not insist on any given alpha or beta levels, and it will evaluate arguments for deviation of either of these from traditionally used values.

More than one justification may be applicable to your proposed animal studies, depending on the mix of observations and experiments you are conducting. Combine non-statistical and statistical justifications as appropriate.

  • When you are not testing a hypothesis or comparing groups of animals, one or more of these Non-Statistical Justifications may be applicable.


Guidance for Non-Statistical Justification of Numbers:

Exploratory/Discovery Studies: (Up to 200 words) For exploratory/discovery work not involving comparisons between groups of animals, numbers are determined by your empirical approach and estimates of numbers of animals necessary to achieve your research goals. Often previously published similar studies provide an estimate of the number which will be required. Provide details in the justification statement. Examples:

  • "We have found in studies of diverse species of wild birds (van Tienhoven et al. 2003) that samples of 25 birds are necessary to characterize patterns of nerve-firing in the Lacoinic ganglion for most species. This sample is required because, despite our best efforts to refine the procedure, the preparation of nerves for recording has only a 75% success rate, and because the animals are variable in the strength of their impulses."
  • "In our studies of the side-preference of avian flight (Emlen 2008, Tienbergen et al. 2005), we have found that roughly 25% of birds prefer left-sided escape from a flight tunnel maze. Because only left-sided birds are valuable for this neurological study, we will fly up to 120 dusty-billed snits through our test maze, stopping when we have collected 25 animals with left-sided escape for our characterization of Lacoinic firing patterns."
  • "As tools to study the control mechanism for this signaling pathway we will generate 18 new transgenic lines (3 artificially fixed expression levels for each of the 6 components of the pathway). Our previous work and similar studies suggest that only 10% pregnancies will result in any viable offspring. We need independently derived founders of each sex (36 individuals for 18 lines). We thus estimate that 360 pregnant females will be needed. We estimate that 360 live offspring will result (10 pups born per viable litter) which we will genotype. 360 females + 360 offspring = 720 for this goal of the protocol."
  • In these exploratory studies, we will determine the effect of a mutation in the largestone gene upon the formation of the kidney. We will initially analyze animals at three different ages: embryonic day 14, when kidney formation is underway, postnatal day 5, when kidney function has just begun, and adulthood. Each mutant kidney will be examined with a minimum of 10 different markers to assay distinct cell-types present within the kidney. At embryonic day 14, given the small size of the organ, one mutant is required per marker. At postnatal day 5, given the growth in organ size, five markers can be tested, and all 10 can be assayed in adult samples. We expect we will require approximately n=7 replicates per marker per time point. Within each mutant litter, we obtain, on average, one mutant and one control animal. We estimate we will require the following number of animals:

E14: 10 markers x 7 replicates x 1 mutant/litter = 70 animals for mutant analysis +70 animals as controls
P5: 10 markers x 7 replicates x 1 mutant/litter divided by 5 markers/mutant = 16 mutants and 16 controls.
Adult: 10 markers x 7 replicates x 1 mutant/litter divided by 10 markers/mutant = 7 mutants and 7 controls

We also expect, however, potential difficulties in generating sufficient numbers of adult samples. ~50% of the mutants die prior to adulthood. We will therefore breed additional animals (~14 mutants and 14 controls aged to adulthood) to accommodate this expected loss. In total, we expect to require 70x2 + 16x2 + 14x2 = 200 animals.

These initial experiments are likely to indicate further studies if a phenotype is observed. For example, we may find that one of our test markers shows that a specific cell-type is strongly affected. We would then require additional animal numbers to test other markers to more closely assess the effect. Similarly, we may find a stronger effect at E14 than during adulthood, indicating a need to pursue more studies at other embryonic stages."

Antibody/Tissue Production: (Up to 200 words) If you are using animals to produce antibodies, other tissue derived factors, cells or tissue, the number of animals needed are determined by the amount of material required for the studies planned and the ability of an individual animal to provide the needed amount. Provide details on the determining factors in the justification statement. Do not just state how many experiments you can carry out in a given amount of time.

Instruction/Teaching/Demonstration: (Up to 100 words) The justification is generally based upon the number of students expected in the course and the number of students that can humanely learn a technique or procedure on a single animal.

The Effect of Expected Complications on Animal Numbers: (Up to 100 words) If applicable, include extra animals to account for expected loss or procedure failure. Example: "We require 10 animals per group in each of the 10 groups for statistical significance. In our experience 20% of the animals will be lost due to unpredictable substrate toxicity. We therefore, increased the total number of animals requested from 100 to 120."

Breeding Colonies: (Up to 300 words) Predicting the number of animals for a breeding colony is often challenging. The justification for total numbers must be based on the number of research animals needed. Cornell University policy is that all vertebrate animals born alive must be counted in animal numbers. Animals should ONLY be counted in USDA category B if they are used solely for breeding. If any procedures are performed on live vertebrates (humane euthanasia, tail snips, blood collection, etc.) they must be counted in USDA categories C, D, or E. Example: mouse pups born alive and either euthanized, or genotyped by tail-snipping, and then euthanized should be counted in USDA category C. 

Pilot Studies: (Up to 100 words) To demonstrate the feasibility of a technique, or if you do not have enough information on the variance or expected difference to perform power calculations, you may perform a pilot study with small numbers of animals. Justify animal numbers based on estimates of numbers of animals necessary to demonstrate feasibility or provide the missing information, or rely on previously published similar studies for an estimate of the number which will be required for the pilot study. If you have significant previous experience with an empirical approach or model, the IACUC will expect you have sufficient data to provide estimates of the variance and expected difference for a statistical power analysis.

Feeder Animals: (Up to 100 words) Protocols utilizing live animals for feed must describe the number of animals to be used for feed. Animal number justification will generally be based upon standard husbandry requirements of the carnivorous species rather than statistical analysis.

Relate, as appropriate the following concepts of the "3 R's" of animal research to your determination of the number of animals you will need.

  • Replacement: Describe why non-animal models or invertebrate models will not suffice for the study.
  • Refinement: Describe why less invasive procedures or procedures which may cause less pain or distress cannot be used.
  • Reduction: Explain how the number of animals you propose to use is the minimum number of animals that will allow you to reach valid scientific conclusions. If you are providing a statistical power calculation this is explicit in that calculation.

Alternatives Search

Purpose: This section is required for protocols with animals in USDA categories D or E.

What the IACUC expects: (250 words or less)

  • Provide a written narrative description of methods and sources used to consider alternatives to procedures that may cause more than momentary or slight pain or distress to animals. State how you determined that alternatives were not available.
  • Address the 3 R's – Replacement (with non-animal systems, or non-vertebrates), Refinement (decreasing or eliminating pain or distress), and Reduction (in number of animals necessary). Relate, as appropriate, the following concepts of the "3 R's" of animal research to your determination of the numbers of animals you will need.
    • Replacement: describe why non-animal models or invertebrate models will not suffice for the study.
    • Refinement: describe why less invasive procedures or procedures which may cause less pain or distress cannot be used.
    • Reduction: explain how the number of animals you propose to use is the minimum number of animals that will allow you to reach valid scientific conclusions. If you are providing a statistical power calculation this is explicit in that calculation.
  • If your protocol has animals from more than one species in USDA categories D or E, please provide separate alternatives searches for each species.

Alternatives Search Help – A reference librarian in the Veterinary Library is available to help you to prepare — or prepare for you — a comprehensive search of the literature when it is required by the Institutional Animal Care and Use Committee (IACUC) in order to submit new or renewal protocols for review and approval. To arrange an IACUC search or consultation, simply contact Reference Services at 607-253-3510 or vetref@cornell.edu.

Purpose: To justify, based on scientific necessity or, in the case of husbandry, veterinary assessment, any deviations from the Guide. Consult a CARE Veterinarian if you have questions.

What the IACUC expects:

  • A detailed description of the deviations from the Standards Care out lined in the Guide. Include the time period for how long this will apply to a given animal.
  • An estimate of the numbers of animals which will be covered by the exemption. If circumstances require a change in this number, please submit an amendment to change this number. The IACUC must review and approve Exemptions From Standards of Care every six months. During Regulatory and Accreditation visits the visitors will expect the numbers housed under the exemption to match the number stated in the protocol.
  • A strong scientific justification for why no existing standard of care is acceptable; or in the case of husbandry considerations, an unequivocal veterinary assessment of the appropriateness of the proposed standards of care.


  • Analgesics must be provided after potentially painful procedures unless the IACUC has PREVIOUSLY approved withholding analgesics as they will irrevocably interfere with research. In this example the IACUC must also consider that unrelieved pain may alter research results.
  • Cage change frequency less than that required in the Guide may be approved based on use of modern technology and an explicit scientific rationale.
  • Frequency of cleaning of housing areas may need to be lower than recommended during certain times during the life cycle of the animal or stage of the research.
  • Agricultural animals used in Biomedical research, may, in some cases, be housed more appropriately in Ag housing rather than in Biomedical housing locations.