How to write the Methods section of a research paper: Examples and guidelines

Contents

• What is the methods section of a research paper?
• Materials and methods vs methods section: what’s the difference?
• Why is the methods section important?
• Methods section vs methodology section: understanding the difference
• When should you write the methods section?
• How to structure the methods section
• What to include in the methods section
• Methods section examples by discipline
• What NOT to include in the methods section
• Avoiding self-plagiarism in the methods section
• Open science practices for the methods section
• Visual aids in the methods section
• Methods section checklist
• Frequently asked questions

What is the methods section of a research paper?

The methods section is the part of a research paper that answers the what, how, which, and why of your study. It describes exactly how the research was conducted in enough detail that a qualified reader could replicate your work. It usually covers the study design, participants or samples, tools and instruments, data collection procedures, and analysis approach.

In a standard manuscript structure (Introduction → Methods → Results → Discussion), the methods section sits between the introduction and the results. It is the backbone of your paper’s credibility: without a clear methods section, readers cannot judge whether your results are valid or reproducible.

Materials and methods vs methods section: what’s the difference?

Many journals, particularly in the life sciences, use the heading “Materials and Methods” rather than simply “Methods.” The distinction matters:

In clinical and social science research, the section is sometimes called “Patients and Methods” or simply “Methodology.” Always check your target journal’s author guidelines for the exact heading required.

Why is the methods section important?

Despite its reputation as the driest part of a manuscript, the methods section carries enormous weight at every stage of the publication process.

• For peer reviewers: This is the primary section used to assess whether the study design is appropriate, the sample size is justified, and the statistical analysis is sound. Incomplete methods are one of the most common reasons for desk rejection.
• For editors: Methods flaws can signal fundamental validity problems that no revision can fix.
• For other researchers: A reproducible methods section is what allows science to build on itself. Researchers attempting to replicate, adapt, or meta-analyze your work depend entirely on what you write here.
• For readers: It establishes trust. A transparent methods section signals that you have nothing to hide about how data was collected or analyzed.

Methods section vs methodology section: understanding the difference

These terms are sometimes confused, particularly in social science and thesis writing:

In most journal articles, you do not need a separate methodology section. The rationale for your approach is embedded within the methods section itself. In a thesis or dissertation, a standalone methodology chapter is usually expected.

When should you write the methods section?

A practical tip that most researchers overlook: write the methods section while you are conducting your experiments, not after. Recording your procedures in real time:

• Prevents you from forgetting small but critical details (exact reagent concentrations, software versions, participant exclusion criteria)
• Captures protocol deviations as they happen
• Saves significant time when drafting the full manuscript

If you submitted a grant proposal or ethics application for the study, those documents are an excellent starting point, but remember to change future tense (“will be conducted”) to past tense (“was conducted”).

How to structure the methods section

A well-structured methods section mirrors the structure of your results section. If you report three experiments in Results, describe those same three experiments in the same order in Methods. This parallel structure makes your paper far easier for reviewers and readers to navigate.

Use subheadings to divide the section. Common subheading categories include:

For very long methods sections, consider placing additional technical detail in supplementary files or on open repositories such as protocols.io (see the Open Science section below).

What to include in the methods section

1. Ethical approvals and informed consent

State this early in the methods section, before describing procedures. Include:

• The name of the ethics committee or institutional review board (IRB) that approved the study
• The approval number or reference
• Whether oral or written informed consent was obtained from participants or their guardians
• For animal studies, the relevant institutional animal care committee approval
• For clinical trials, the trial registration number (e.g., ClinicalTrials.gov)

2. Study design and rationale

Don’t just name your design but briefly justify it. For example, explain why a case-control study was chosen over a cross-sectional design, or why a within-subjects design was used. This is especially important for less common or novel approaches.

Example of a purposeful methods sentence:

To compare working memory performance across exercise intensities, a counterbalanced, randomized controlled within-subject design was employed, which controlled for order effects and individual baseline differences.

This is stronger than simply stating: “A randomized controlled within-subject design was employed.”

3. Participants or samples

Include all details relevant to reproducibility and generalizability:

• Total number of participants/samples; how sample size was determined (power calculation)
• Inclusion and exclusion criteria, and the rationale for them
• Recruitment method (random sampling, convenience sample, purposive sample)
• Demographic details relevant to the study (age, sex, disease status, species and strain, etc.)
• Drop-out or exclusion figures with reasons

4. Materials, instruments, and apparatus

Provide enough detail that someone else could source the same materials:

• Reagents: name, concentration, supplier, catalog number, lot number where relevant
• Instruments: name, model, manufacturer, city, country
• Software: name, version number, developer
• Questionnaires: full name, version, scoring method, validation reference. Specify if a translated version was used, and if yes, cite the studies showing the validity and reliability of the translated version.
• Cell lines: name, source, passage number, authentication method
• Animals: species, strain, age, sex, weight, housing conditions

Where a material has a Research Resource Identifier (RRID), cite it. RRIDs are persistent identifiers for antibodies, cell lines, model organisms, and software tools (searchable at scicrunch.org/resources). An increasing number of journals now require them.

5. Procedures in chronological order

Present experimental procedures in the order they were performed. Begin each paragraph or subsection with a statement of purpose, i.e., why this step was taken, before describing how it was done.

Before (no purpose statement):

X-ray diffraction was performed on samples with 1, 3, and 5 wt.% Cu.

After (with purpose statement):

To compare the elemental composition across copper concentrations, X-ray diffraction (Bruker D8 Advance, Bruker AXS, Karlsruhe, Germany) was performed on samples with 1, 3, and 5 wt.% Cu.

6. Variables

Clearly define all four types:

Addressing confounding variables (and explaining how you controlled for them) is a common weakness in methods sections and a frequent cause of reviewer comments.

7. Outcome measures: validity and reliability

For any measurement tool (scale, questionnaire, instrument), state:

• The evidence supporting its validity for this population
• The reliability metric (Cronbach’s alpha, intra-class correlation, test-retest reliability)
• Any adaptations made to a standard tool and why

8. Sample size and power calculation

Always state the estimated sample size and how it was calculated. Include:

• The expected effect size (based on prior literature)
• The alpha level (typically 0.05)
• The desired statistical power (typically 80–90%)
• The software or formula used for the calculation

9. Statistical analysis

Describe every statistical test used. “We used a t-test” is not sufficient; you should specify:

• The type of test (independent samples t-test, paired t-test, etc.)
• Whether assumptions were tested (normality, homogeneity of variance)
• The significance threshold (e.g., α = 0.05, two-tailed)
• Software and version (e.g., SPSS v.28, IBM, Armonk, NY; R v.4.3.1)
• For Bayesian analysis: prior distributions and Bayes factor thresholds

10. Reporting guidelines and checklists

Using a published checklist strengthens your methods section and signals rigor to editors. Key checklists by study type:

Methods section examples by discipline

Biomedical and clinical research

Biomedical methods sections typically follow a strict IMRaD format. Begin with study setting and time period, followed by patient recruitment, study design, randomization (if any), intervention details, outcome measures, and statistical analysis. Use the CONSORT or STROBE checklist as your writing guide.

Qualitative and social science research

Qualitative methods sections follow different conventions from quantitative ones. You are expected to:

• Justify your research paradigm: explain why an interpretive or constructivist approach is appropriate for your research question
• Describe your positionality: acknowledge your relationship to the subject matter and how it may influence interpretation
• Detail your sampling strategy: purposive, snowball, or theoretical sampling, and why
• Describe the data collection method: semi-structured interviews, focus groups, ethnographic observation, document analysis
• Explain your analysis approach: thematic analysis, grounded theory, discourse analysis, IPA. Cite the methodological framework you followed (e.g., Braun & Clarke, 2006 for thematic analysis)
• Address trustworthiness: the qualitative equivalent of validity and reliability; include member checking, triangulation, or thick description as appropriate

Thesis and dissertation methods chapters

A methods section in a journal article is typically 300–800 words. A thesis or dissertation methodology chapter is considerably longer (2,000–5,000+ words) and includes additional elements:

• A full literature review of methodological options considered and why they were rejected
• A philosophical underpinning (positivism, interpretivism, critical realism, etc.)
• Researcher reflexivity statement
• Detailed ethical considerations beyond a simple IRB statement
• Data management and storage plan

What NOT to include in the methods section

Avoiding self-plagiarism in the methods section

If you have published papers using the same methods before, it is tempting to copy that description directly. This is considered text recycling or self-plagiarism, and most journals’ plagiarism-detection software will flag it, even when the words are your own.

How to handle repeated methods:

• If the method is identical and well-published: Cite your previous paper and write: “[Procedure] was performed as described previously [citation], with the following modifications: …”
• If the method is the same but the study differs: Rewrite the description from a different angle, emphasizing the aspect most relevant to the current study’s aim.
• If the journal explicitly permits text recycling for methods (some do): Follow their stated guidelines and disclose the overlap in your cover letter.

The Committee on Publication Ethics (COPE) has published guidelines on text recycling that are worth reading before submitting to any journal.

Open science practices for the methods section

Modern journals increasingly expect methods sections to support reproducibility beyond the manuscript itself. Best practices include:

• Deposit detailed protocols on protocols.io. This platform assigns each protocol a DOI, which you can cite directly in your methods section. You can update the protocol after publication, and future researchers can fork and adapt it.
• Cite RRIDs for all key biological reagents, cell lines, model organisms, and software tools. Example: “Anti-CD3 antibody (RRID: AB_394081)”
• Link to data repositories. Raw data, code, and analysis scripts should be deposited in appropriate repositories (OSF, Zenodo, Figshare, GitHub) and referenced in the methods section
• Use ORCID identifiers for all authors to ensure attribution is persistent and unambiguous
• Register your study prospectively (for clinical trials and some observational studies) and cite the registration in the methods

Visual aids in the methods section

Complex methods benefit from visual representations. Common options:

At submission, figures usually go in a separate file or at the end of the manuscript, but you should reference them in the body of the methods section (e.g., “Participant flow is shown in Figure 1”). Check your journal guidelines about placement of figures and tables.

Methods section checklist

Use this before submitting your manuscript:

Content

• Ethical approval and informed consent stated
• Study design described and justified
• Participant/sample details including inclusion and exclusion criteria
• Sample size estimation and power calculation provided
• All materials, instruments, and software listed with full details
• Procedures described chronologically with purpose statements
• All variables (independent, dependent, control, confounding) defined
• Validity and reliability of outcome measures addressed
• Statistical tests fully described with software and version
• Reporting guideline checklist completed and attached

Format and language

• Written in past tense throughout
• Subheadings used to organize the section
• Methods order matches results order
• Citations included for all previously published procedures
• No results or evaluative commentary present
• Supplementary materials referenced where used
• No self-plagiarism (text recycled from own prior papers)

Frequently asked questions

How long should the methods section be?

For a journal article, aim for roughly 15–20% of the total manuscript length. A typical 4,000-word paper would have a methods section of 600–800 words. Thesis methodology chapters are much longer — often 2,000–5,000 words.

Should the methods section use subheadings?

Yes, in most cases. Subheadings (Participants, Materials, Procedure, Statistical Analysis, etc.) help reviewers quickly locate the information they are looking for and make the section easier to navigate.

What tense should the methods section be written in?

Past tense throughout, because you are reporting what was done during the study. Common error: copy-pasting from a grant proposal (which is written in future tense) without updating.

Can the methods section include figures or tables?

Yes. Participant flow diagrams, schematic figures of experimental setups, and demographic tables are all common in methods sections. At submission, check whether your target journal requires them to be embedded or placed at the end.

Can the methods section contain citations?

Yes, and it should. Cite previously published protocols you followed, the original papers describing validated instruments or scales, and the sources for reporting guidelines you used.

What is the difference between the methods section and the methodology section?

The methods section describes what you did. The methodology section (used mainly in theses and qualitative research) discusses why you chose that approach and the philosophical framework underlying it.

Can I use first person and active voice in the methods section?

This depends on the journal’s style guide. Some journals prefer passive voice (“samples were analyzed”); social science and humanities journals increasingly accept or prefer active voice (“we analyzed samples”). Always check the target journal’s author guidelines.

How do I write a methods section for a study that uses a standard protocol?

Cite the original protocol reference, state that you followed it, and describe any modifications in detail. For example: “RNA extraction was performed following the manufacturer’s protocol (Qiagen RNeasy Mini Kit, Hilden, Germany) with the following modifications: …”

What is a methods section for a qualitative study?

In qualitative research, the methods section (or methodology chapter) describes the research design (e.g., thematic analysis, grounded theory), data collection approach (interviews, observation), sampling strategy, analysis process, and how trustworthiness was ensured. It also typically includes a positionality statement.

How do I handle methods that are the same as a previous paper I published?

Cite your previous paper and briefly describe the method, noting it was performed as previously described. Avoid copying sentences verbatim to prevent text recycling flags from journal plagiarism detectors. Consult the COPE text recycling guidelines if unsure.

This article was originally published on September 18, 2018, and updated on May 13, 2026.