How to Write a Research Protocol: A Step-by-Step Guide for Medical Research

Most first research projects get stuck here. It is an idea that has been thought of, approved by the supervisor and then, “Where’s your protocol?” Need help writing a research protocol? Here’s how to do it.

A protocol is a complete study plan, written prior to the collection of any data. It covers your research question, aims, design, methods, data collection, data analysis and how you will ensure the protection of your participants. Most funders require it, and ethics committees (IRB/REC) will not approve any study without one! It also maintains the truthfulness of the person, because one can easily check if the plans were met or not.

This guide will provide you with an understanding of what a research protocol is and a step-by-step formula for how to create one.

What is a Research Protocol?

A research protocol is a document which has details about the purpose, design, methods, participants, manner of data collection, data analysis, and ethical issues of a research study.

Why so much detail? A study usually involves a number of people working for several months. Everyone working from the same document will collect data in the same way each time, participants will be protected, and another team can repeat the study at another time (that’s “reproducibility”).

“Proposal” is a term that is used interchangeably with “protocol”. The questions “what” and “why” are answered in a proposal. Protocols are your answer to the question “how”. 

That is, it is detailed enough for someone else to be able to conduct your study.

What are the elements of a research protocol?

The majority of protocols are similar. Most medical research protocols will have these 10 sections (they may be referred to differently at various institutions).

1. Title Page and General Information

• Specific title including identification of the study topic, the population and the design of the study.
• The principal investigator (lead researcher) and co-investigators (other researchers)
• Sources of funding and institutional affiliations
• A protocol ID number, version number and date

2. Abstract/ Project Summary

A summary of the context, aim, methodology, sample and results of the research project.

Usually broken into parts based on the headings of your institution

3. Introduction and Background

• Describe the health problem(s) being studied, and provide a brief summary of previous research.
• Discuss what is not known and what needs to be done.
• State the need for your study and the persons who may benefit from your study.

4. Research goals and research hypothesis.

If your study is testing a hypothesis (a prediction), then write your prediction.

Use the SMART acronym to set SMART goals.

5. Study Methodology

The things to consider when designing a research or when determining the context.

• The target population and the participants are described.Target population and participants described.
• Who (and who is not) is to be included?
• Sampling techniques and sample size.
• The collection methods used, and study procedures.

6. Outcomes and Endpoints

• Main outcome: what is the main outcome you will use to evaluate the result of your research.
• Secondary outcomes: Other outcomes of interest
• The duration of time points/methods of evaluation (baseline, 6 months etc.)

7. Statistical Analysis Plan

• Statistical software
• Descriptive analysis (summarising data) and inferential analysis (testing relationships)
• Confidence intervals, level of significance (p < 0.05)
• What you will do if there are missing data

8. Ethical Considerations

• IRB or REC approval
• Informed consent process
• Confidentiality and safety of participants including how to maintain confidentiality.

9. Timeline and Budget

• Estimate the length of time each stage of the research process will take (recruitment, analysis, etc.)
• Staff, equipment and estimated expenses.

10. References and Appendices

• A uniform referencing system (eg Vancouver).
• Questionnaires, consent forms, data collection tools and other documents to support the data collection process.
• Writing a Research Protocol Step by Step covers the stages of writing a research protocol in detail.

Understanding What’s in a Protocol: The Order in Which to Write It.

Step 1. Outline a Research Question

Begin with a clinically relevant question, with a logical answer. Use the PICO framework for studies testing an intervention:

Understanding the difference between a research question and hypothesis is essential when developing a clear and focused research protocol.

• The group of the population being studied.
• A treatment or an exposure to the treatment.
• Comparing it to something: what it is compared to
• Outcome: Product that is being evaluated
• Is structured lifestyle counseling superior to routine care at 6 months in regard to glycated hemoglobin (HbA1c) levels in adults with type 2 diabetes?

A different framework might be required for other designs, such as qualitative studies.

Step 2. Complete a Literature Review. 

• Use the PubMed and other appropriate databases (Google Scholar) to search.
• Developing an effective literature search strategy is essential for identifying relevant studies. Learn how to build a PubMed search strategy using MeSH terms to find relevant medical research more systematically.
• Document important current knowledge and investigations that need to be expanded.
• Explain and develop procedures using previous work.
• Use a reference manager (e.g. Zotero or Mendeley).

Step 3. Define study objectives and a hypothesis

State one clear and specific main goal.

• Utilize secondary goals (if available).
• Make a statement of a hypothesis that can be tested if necessary.
• Make sure all the objectives relate to your research question.

Step 4. Choose an Appropriate Study Design

• Cross-sectional study: the exposure and outcome are measured concurrently.
• A collection of individuals over time who have a similar set of personalities and who can achieve the outcome.
• Case-control study: compares the history of exposures of individuals with a condition with the exposures of individuals without a condition.
• Randomized controlled trial (RCT): randomly assigns patients to an intervention or control group.
• Qualitative study: looks into experiences and opinions via interviews or focus groups.

Select a design which is appropriate for your question, resources, time and moral constraints. 

Step 5. Determine Sample Size and Sampling Method

• Include the target population and inclusion/exclusion criteria.
• Choose a sampling method (random, consecutive).
• Estimate the sample size for the primary outcome, the required effect size, the variability, the power (usually 80%) and the significance level.
• Accurate sample size estimation is important for ensuring that your study has sufficient statistical power. Learn more about sample size calculation for clinical research, including effect size, statistical power, and significance levels.
• Have extra participants to accommodate the possibility of non-response and dropouts.

Step 6. Make the Data Collection & Analysis Plan

• Describe how and what your data collection methods will be.
• Describe each variable and outcome measure.
• Determine the statistical testing or qualitative methods to use.
• Identify the computer program(s) to be used (e.g., SPSS, R, Stata, etc.).

Step 7. Address the Ethical issues and develop the timeline

• Create informed consent and participant information sheet.
• Recognize possible hazards and how you will maintain confidentiality.
• Set deadlines for submitting ethics, recruitment, data collection, data analysis and publication.
• Ensure all approvals prior to using human subjects.

The format and template used for writing a research protocol for medical students

This is a straightforward outline of a research protocol for medical students. It is also a simple clinical research protocol template that can be used as a basic research protocol. Do not alter the order of the sections as this would make it difficult for the reviewers to find the information.

Section	What to include
Title page	Study title and investigators
Abstract	Study summary
Introduction	Background and rationale
Objectives	Primary and secondary objectives
Hypothesis	Research hypothesis, if applicable
Methodology	Design, setting, and population
Sample size	Calculation and sampling method
Eligibility	Inclusion and exclusion criteria
Outcomes	Primary and secondary endpoints
Data collection	Instruments and procedures
Analysis	Statistical analysis plan
Ethics	Consent and ethical approval
Timeline	Research milestones
Budget	Estimated expenses
References	Cited literature
Appendices	Questionnaires and consent forms

The requirements are different in different areas. First, make sure that your university, hospital, funding agency, or ethics committee has specific formatting requirements. There are lots of institutions that have their own template and when you use one of their templates, it saves time since reviewers have an idea of where to look.

Key Components of a Research Protocol and Their Importance in obtaining  Ethical Approval.

The ethics committee is interested in the scientific soundness of your research, the fact that people will not be harmed by it and the fact that someone will be responsible for conducting the research. The following should be included in your protocol:

• The study may be taken to an Institutional Review Board (IRB) or Research Ethics Committee (REC) for review of the study.
• A participant information sheet and informed consent form must be in the language that is understood by the participants.
• Risks that might occur and benefits that could be expected
• How the information will be secured against disclosure and how the information will be secured in storage.
• Who will be recruited, how and what will be done to ensure vulnerable people, such as children, prisoners or people who cannot give consent for themselves are protected.
• How adverse events are to be reported (harmful or unexpected events) and monitored (where appropriate)
• Sources of funding and any conflicts of interest will be identified.

Prior to undertaking any research activity that requires an ethical review, you will need approval. Depending on the type of study you’re conducting and your institution, there may be specific needs that arise; talk to your committee early on to get their guidance.

Which Research Protocol Guidelines to Follow?

There are a number of guidelines and registries related to research protocols and novices frequently confuse these. Every one has an individual role to play.

Guideline	Application
SPIRIT 2025	Randomized trial protocols
PRISMA-P	Systematic review and meta-analysis protocols
CONSORT	Reporting randomized trial results
STROBE	Reporting observational studies
EQUATOR Network	Directory of reporting guidelines
PROSPERO	Prospective registration of eligible systematic reviews
ClinicalTrials.gov	Registration of applicable clinical studies and trials

These are a few things to take into consideration:

• The replacement of SPIRIT 2013 is called SPIRIT 2025 and contains a list of 34 minimum items that a trial protocol should include.
• PRISMA-P is a 17 item checklist created for systematic review protocols.
• PROSPERO is not a writing checklist. Spend time registering your review before the data extraction starts.
• Researchers planning eligible systematic reviews should understand the registration process before starting their review. Read our guide on how to register a systematic review on PROSPERO to understand the preparation and registration requirements.
• CONSORT and STROBE are guidelines for reporting completed randomized and observational studies, respectively, but NOT for protocol writing.

Choose your guideline that corresponds to your study design and to your stage (planning or reporting).

The Following are Common Mistakes to Avoid When Writing a Research Protocol:

The majority of protocol problems are due to small planning gaps that reviewers are on the lookout for and quickly find. Watch for these:

• Research question is too general or too specific
• Objectives that are not aligned with the primary outcome
• A study that does not address your question:
• No sample size calculation or explanation given for the size.No explanation of the sample size or calculation thereof.
• Too weak information regarding data collection and statistical analysis
• Not obtaining information regarding informed consent, confidentiality or ethical approval.
• The protocol must be coherent and consistent within itself. The research question and aims should be linked to the same purpose as the research methods, outcomes and analysis. When one part changes, change the others.

FAQs

Q1. How many parts will be there in a research protocol?

Introduction, aim, method, ethic and data analysis.

Q2. What is the length of a research protocol?

No word or page count can be provided. The length will vary based on your study’s complexity and what your institution needs. CPIH protocol for a simple student study will generally be shorter than the multi-center clinical study.

Q3. Do medical students have the ability to write a research protocol?

Yes. Medical students can write protocols with advice from a research supervisor and institutional advice.

Q4. Do ethics approvals for a research protocol need to be obtained?

Many human research studies have an elaborate protocol for ethical review, but this is not always the case, depending on the type of study and institution.

Q5. What is the difference between SPIRIT and PRISMA-P?

SPIRIT is designed for protocol designs of randomized trials. PRISMA-P is a protocol for systematic reviews.

Conclusion

A good research protocol helps you to know how to conduct science-based, practical and ethical research. Follow a standard protocol format AND use the correct reporting guideline depending on the type of study design, get institutional approval before beginning. Proper protocol time invested up front will prevent issues from occurring later that can cost the company.

Looking to write your first protocol with expert assistance? Learn research methods step-by-step with the American Academy of Research and Academics (AARA) and experienced researchers.

Sources:

1. World Health Organization. Recommended format for a research protocol. Research Ethics Review Committee. https://www.who.int
2. Chan AW, Boutron I, Hopewell S, et al. SPIRIT 2025 statement: updated guideline for protocols of randomised trials. BMJ. 2025;389:e081477. https://doi.org/10.1136/bmj-2024-081477
3. Moher D, Shamseer L, Clarke M, et al. Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst Rev. 2015;4:1. https://doi.org/10.1186/2046-4053-4-1
4. Centre for Reviews and Dissemination, University of York. PROSPERO: Guidance for registering human studies. https://www.crd.york.ac.uk/prospero/
5. National Institutes of Health. Clinical trial protocol templates. https://grants.nih.gov
6. UCSF Clinical and Translational Science Institute. Clinical trial protocol development. https://ctsi.ucsf.edu
7. EQUATOR Network. Library of reporting guidelines. https://www.equator-network.org
8. ClinicalTrials.gov. U.S. National Library of Medicine. https://clinicaltrials.gov

Disclaimer:

Articles published by American Academy of Research & Academics are prepared by our team using information from direct experience, publicly available resources, and educational references. AI tools may be used to assist with drafting, proofreading, and formatting; however, all content undergoes review and approval before publication.
The information provided is intended for educational purposes only. Requirements, policies, and processes may change over time. Readers should consult official sources for the most current information.