How to Write the Methods Section of a Research Paper
A complete guide to writing a reproducible, journal-ready methods section: what to include, how much detail, reporting standards, and common mistakes.
The methods section is the most scrutinized section by peer reviewers assessing methodological rigor, and the most important section for reproducibility. A weak methods section raises doubts about the validity of your results. A strong one builds reviewer confidence and enables others to build on your work. This guide covers exactly what belongs in a methods section, at what level of detail, and how to meet reporting standards across disciplines. Before submitting, run your full paper through our manuscript checker to catch methods section issues automatically.
What belongs in the methods section
The methods section must include everything a reader would need to evaluate and replicate your study. Standard components include:
- Study design
- experimental, observational, qualitative, computational
- Participants or materials
- who or what was studied, selection criteria, sample size
- Procedures
- exactly how data was collected, in chronological order
- Measures or instruments
- what was measured and how, including reliability/validity information
- Analysis
- statistical methods, software, significance thresholds, how missing data was handled
- Ethical approval
- IRB/ethics committee approval statement
Level of detail required
The methods section should provide enough detail that a competent researcher in your field could replicate the study. This is the reproducibility standard. Established standard procedures can be cited rather than described fully ('We used the protocol described by Smith et al., 2020'). Novel procedures require full description. Err on the side of more detail: reviewers rarely complain that methods are too detailed, but frequently ask for more.
Reporting standards by discipline
Many disciplines have formal reporting guidelines that specify what must appear in the methods section. Medical and clinical research: CONSORT (RCTs), STROBE (observational), PRISMA (systematic reviews). Psychology: APA JARS (Journal Article Reporting Standards). Animal research: ARRIVE 2.0. Qualitative research: COREQ or SRQR. Check whether your target journal requires a completed reporting guideline checklist.
How to describe participants or subjects
For human participants: report sample size, inclusion/exclusion criteria, recruitment method, and relevant demographics (age, gender, clinical characteristics where relevant). For animal subjects: species, strain, age, sex, housing conditions. For computational studies: dataset name, size, source, preprocessing steps. Avoid reporting only what is convenient; journals expect transparent participant description.
Statistical analysis reporting
Statistical methods must be specified precisely: the name of each test used, software and version, significance threshold (α level), how multiple comparisons were handled, and how missing data was addressed. Report exact p-values (e.g., p=0.023), not just 'p<0.05'. Include effect sizes alongside significance tests. For regression analyses, specify which variables were included and why.
Common methods section mistakes
Most frequent methods issues identified by reviewers:
- Missing sample size justification (power calculation)
- Insufficient participant description, specifically who was included and excluded
- Software and version not specified
- Statistical tests named without specifying assumptions or how they were tested
- Missing IRB/ethics statement for human subjects research
- Past/present tense inconsistency; methods should be in past tense
- Procedures described in the results section instead of methods
Frequently asked questions
Yes: the methods section describes what you did, so use past tense throughout ('Participants were recruited...', 'Data were analyzed using...'). Present tense is used in the results and discussion for interpreting findings.