How to Write a Methods Section for Clinical Research: A Guide for Researchers

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If you’ve ever followed a recipe to cook a dish, you already understand the purpose of a methods section. Just like a recipe tells you exactly what ingredients and steps to follow, the methods section of a research paper explains how the study was conducted so others can replicate it, evaluate its reliability, or build upon it.

For new researchers, the challenge is finding the right balance — enough detail so readers understand and trust your work, but without turning it into an overwhelming list of technical notes. In this guide, we’ll walk through the core parts of a methods section, explain why each one matters, and give you examples so you can strike the perfect balance with your own writing.

To make this easier, you can download free manuscript templates that come with structured Methods sections built in.

What Is a Methods Section and Why It Matters

Purpose in academic writing

The methods section is where you show your work. It demonstrates that your research was conducted systematically and ethically, and it gives readers a way to judge whether your results are valid.

What readers expect to find

Depending on your field, readers generally look for:

• How the study was designed
• Who or what was studied
• What tools or materials were used
• How the study was carried out
• How the data was analyzed

If someone with similar resources wanted to reproduce your study, they should be able to do so after reading your methods.

The Core Elements of a Strong Methods Section for Clinical Research

1. Ethics Approval

Describe how ethical approval was obtained and provide the approval number. Briefly outline the informed consent process. Note that not all studies require ethics approval—for example, systematic reviews or research using publicly available data often do not require consent. In such cases, include a statement explaining the waiver and confirming compliance with local ethics board requirements.

Example: “Ethics approval was obtained from the XX Research Ethics Board (Approval #324132). Informed consent was obtained by trained research personnel prior to enrollment.”

2. Reporting Guideline Adherence

Reporting guidelines are structured checklists that help ensure research manuscripts are complete and transparent. They outline the essential information authors should include so readers can fully understand what was done in the study—and just as importantly, what was not. Indicate which guideline you followed (e.g., STROBE for observational studies, CONSORT for randomized controlled trials, PRISMA for systematic reviews) and state this explicitly.

Example: “This study was designed and reported in accordance with the STROBE statement.”

As a best practice, complete the appropriate EQUATOR Network checklist for your study type and submit it with your manuscript. You can also try our reporting guideline checker tool here for free.

3. Research design

Be explicit about the overall design, including prospective vs. retrospective and, if observational, the specific subtype (e.g., cohort, case-control, cross-sectional, or case series). Clearly state the clinical or research setting, timeframe, and study purpose.

Examples:

• “We conducted a prospective cohort study in the ICU to evaluate the association between XX disease and YY outcome.”
• “We performed a retrospective case-control study using hospital records to compare patients with XX disease to matched controls without the disease.”
• “This was a case series describing all patients admitted with XX disease during a six-month period.”

4. Setting

Readers need to know where your study took place and the context of that environment. Describe the hospital, clinic, or dataset setting in enough detail that others can judge the generalizability of your results. Mention whether the institution is academic or community-based, its geographic location, and any relevant specialized services.

Example:

“Patients were recruited at XXX Hospital, an academic tertiary-care hospital in City, Country, from January 202X to June 202X. The hospital includes specialized services such as a cardiac catheterization lab and a regional trauma program.”

5. Participants

This section should explain how patients or datasets were identified and recruited, without reporting descriptive statistics (which belong in the Results). Begin by clarifying your sampling approach—was it consecutive, convenience-based, or random? Then outline how screening was done and list the inclusion and exclusion criteria explicitly.

Example:

“A consecutive sample of patients presenting with XX disease within 24 hours of admission were screened. Patients were eligible if they were ≥18 years and admitted to the ICU. Exclusion criteria included pre-existing condition YY or inability to provide informed consent.”

6. Data Collection

Describe the process by which your study data were gathered so that readers could, in theory, replicate it. Key details include who collected the data, the tools and instruments used, and the timing and frequency of collection. Also note how data quality was ensured—such as double data entry or independent verification.

Example:

“Data were extracted from electronic health records using standardized case report forms by trained research assistants. Variables included demographic, clinical, and laboratory data. To ensure accuracy, 10% of records were independently checked by a second abstractor.”

7. Outcomes

Your outcomes are the anchor of your study. Define your primary outcome clearly, since your study design and statistical analysis should be powered around it. Then list secondary outcomes that provide supporting or exploratory information.

Example:

“The primary outcome was all-cause in-hospital mortality. Secondary outcomes included ICU length of stay and the need for renal replacement therapy.”

8. Statistical Methods

The statistics section should tell readers not just which tests you ran, but also how you treated different types of variables and what software you used. Clarify how you summarized continuous versus categorical data, and set your threshold for statistical significance. This section reassures reviewers that your analysis was rigorous and reproducible.

Example:

“All analyses were performed in Stata version XX. Continuous variables were summarized as mean (SD) or median (IQR) as appropriate, while categorical variables were reported as counts and percentages. Two-sided p-values <0.05 were considered statistically significant.”

9. Multivariable Analysis

If your study used regression or other multivariable approaches, explain how you selected variables and built the model. Was selection based on prior literature, clinical reasoning, or data-driven criteria? Being transparent here helps readers judge whether the model was overfitted or biased.

Example:

“Variables for multivariable logistic regression were selected a priori based on clinical relevance and previous literature.”

10. Sample Size Calculation

Finally, if you performed a sample size calculation, report how it was done and what assumptions were used. Even in retrospective studies, mentioning whether a sample size justification was considered signals careful study planning. Even for pilot studies, calculators like this are useful to ensure you are adequately powered to meaningfully draw conclusions regarding efficacy, feasibility, or safety.

Example:

“A sample size of XX participants was required to detect a clinically meaningful difference in YY outcome, assuming α=0.05 and 80% power.

Writing Tips for Clarity and Transparency

Clarity in the Methods section is what makes your research reproducible and credible. A few guiding principles can go a long way:

• Be detailed enough to allow replication. If another researcher cannot reproduce your work based on what you’ve written, you’ve left out essential details.
• Write in past tense. Remember, you are describing what you did, not what you are doing now.

Common Pitfalls and How to Avoid Them

Even well-designed studies can lose credibility if the Methods section is poorly written. Here are three common pitfalls to watch for:

• Missing key details. Avoid vague statements like “participants completed a questionnaire.” Instead, specify the exact questionnaire, number of items, and whether it was validated.
• Mixing results into methods. Keep the Results section separate. Methods should describe the “how,” not the “what happened.”
• Overloading with irrelevant information. If a detail doesn’t affect reproducibility or interpretation, it doesn’t belong. Focus only on what matters for replication and understanding.

Final Thoughts on Writing Excellent Methods Sections

Think of your Methods section as a blueprint for replication. If another researcher could follow your description step by step and arrive at the same dataset, you’ve achieved the right level of clarity. By focusing on study design, setting, participants, data collection, outcomes, and analysis, you provide readers with a transparent roadmap of your work.

To make this process easier, you don’t have to start from scratch. These free manuscript templates come pre-structured with Methods sections that you can adapt for your own research, giving you a head start on organization and completeness.

If you’d like an added layer of assurance, Resub’s copy-editing and automated reformatting tools can help refine clarity, tighten structure, and ensure adherence to journal guidelines before submission. That way, you can spend less time worrying about formatting details and more time focusing on your science.

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