How to Write the Methods Section of a Systematic Review: PRISMA Checklist Guide

The methods section of a systematic review describes exactly how you identified, selected, appraised, and synthesized the evidence. Under PRISMA 2020 (Page et al., 2021), the methods section spans Items 5 through 16, covering everything from eligibility criteria to certainty assessment. A well-written methods section allows any reader to replicate your review, and it is the section that peer reviewers scrutinize most closely. If a reviewer cannot follow your methods, they will reject the manuscript regardless of your findings. This guide covers each PRISMA 2020 methods sub-item in order, provides example sentences you can adapt, flags the most common reviewer criticisms for each section, and explains how to report protocol deviations and cite the tools you used.

Before writing your methods section, you should have a registered protocol, a completed search, and finalized data extraction. If you have not yet reached that stage, start with our step-by-step guide to writing a systematic review for the full workflow from question formulation to manuscript submission.

Eligibility Criteria: PRISMA 2020 Item 5

PRISMA 2020 Item 5 requires you to specify the inclusion and exclusion criteria for your review, including the study characteristics (population, intervention, comparator, outcome, and study design) and the report characteristics (language, publication status, and date range). The Cochrane Handbook (Higgins et al., 2023) recommends structuring eligibility criteria around the PICO framework (or PECO for observational reviews), which ensures every element of your research question maps directly to a criterion.

What this subsection must contain:

• The population, intervention or exposure, comparator, and outcome definitions, stated with enough specificity that a second reviewer could independently apply them
• The study designs eligible for inclusion (randomized controlled trials only, or observational studies as well)
• Any restrictions on language, publication date, or publication status (conference abstracts, preprints, grey literature)
• Justification for each restriction, because reviewers will question any limitation that could introduce selection bias

Example paragraph:

Common reviewer criticisms:

• "The eligibility criteria are vague. How do you define 'structured exercise'?" Reviewers want operational definitions, not general terms.
• "Why did you exclude non-English studies? This could bias your results." Always justify language restrictions with a citation or practical rationale.
• "You did not specify the minimum follow-up period." If your outcome requires a time horizon, state it explicitly.

Use our free inclusion and exclusion criteria builder to structure your PICO or PECO elements into a formatted criteria table before drafting this section.

Information Sources: PRISMA 2020 Item 6

PRISMA 2020 Item 6 requires you to list all databases, registers, websites, organizations, reference lists, and other sources you searched or consulted to identify studies. You must also report the date of the most recent search for each source. The Cochrane Handbook recommends searching at least MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials (CENTRAL) for intervention reviews, plus discipline-specific databases relevant to your topic.

What this subsection must contain:

• The full name of every database searched (not just abbreviations)
• The platform or interface used for each database (for example, "MEDLINE via PubMed" or "MEDLINE via Ovid")
• The date of the last search for each database
• Any additional sources: trial registries (ClinicalTrials.gov, WHO ICTRP), grey literature databases (OpenGrey, ProQuest Dissertations), reference lists of included studies, forward citation tracking, and contact with study authors

Example paragraph:

Common reviewer criticisms:

• "You searched only one database. This is insufficient for a systematic review." Two databases is the bare minimum; three or more is standard.
• "You did not report the search dates." Without dates, the review is not reproducible.
• "Why did you not search Embase? You may have missed European and pharmacological literature." Justify any omission of major databases.

Search Strategy: PRISMA 2020 Item 7

PRISMA 2020 Item 7 requires you to present the full search strategy for at least one database, including any filters or limits used. The complete search strategies for all databases should be available in a supplementary file. This is where many methods sections fail, because authors provide only a list of keywords rather than a reproducible search string with Boolean operators, MeSH terms, and field tags.

What this subsection must contain:

• A statement that the full search strategy is available in a supplementary appendix
• The key concepts combined with Boolean operators (AND, OR)
• Whether controlled vocabulary (MeSH, Emtree) was used alongside free-text terms
• Any filters applied (study design filters, date limits, language filters)
• Whether a librarian or information specialist developed or peer-reviewed the search strategy, and if so, using which framework (such as the PRESS checklist)

Example paragraph:

Common reviewer criticisms:

• "The search strategy is not reproducible. You listed keywords but did not show the actual search string." Always include the full string with Boolean logic and field tags.
• "You did not use controlled vocabulary. Free-text only searches miss indexed records." Combine MeSH/Emtree with free-text for comprehensive retrieval.
• "There is no evidence the search was peer-reviewed." Librarian involvement and PRESS review strengthen credibility.

Build your search strings systematically using the free online search strategy tool, and refer to our search strategy methodology for detailed instructions on combining controlled vocabulary with free-text terms across multiple databases.

Selection Process: PRISMA 2020 Item 8

PRISMA 2020 Item 8 requires you to describe the process used to select studies for inclusion, including the number of reviewers at each stage, how disagreements were resolved, and any automation tools or software used. The Cochrane Handbook mandates independent dual screening at both the title-abstract and full-text stages.

What this subsection must contain:

• How many reviewers independently screened titles and abstracts, and how many screened full texts
• The software or tool used for screening (Covidence, Rayyan, Abstrackr, or manual spreadsheet)
• How disagreements between reviewers were resolved (discussion, third reviewer, consensus)
• Whether a calibration or pilot screening exercise was conducted before formal screening began
• The inter-rater reliability statistic, if calculated (Cohen's kappa or percentage agreement)

Example paragraph:

Common reviewer criticisms:

• "Only one reviewer screened the records. This introduces selection bias." Single-reviewer screening is a critical methodological weakness.
• "You did not describe how disagreements were resolved." Always state the resolution mechanism.
• "What software did you use? This affects reproducibility." Name the tool and version.

Data Collection Process: PRISMA 2020 Item 9

PRISMA 2020 Item 9 covers how data were extracted from included studies, including the number of reviewers who independently extracted data, how disagreements were handled, any automation tools used, and how missing data were obtained from study authors.

What this subsection must contain:

• The number of reviewers who independently extracted data
• Whether a standardized data extraction form was used, and if it was piloted
• The specific data items extracted (see Item 10 for the list)
• How discrepancies between extractors were resolved
• Whether and how study authors were contacted for missing or unclear data

Example paragraph:

Common reviewer criticisms:

• "Data were extracted by only one reviewer. This is a significant limitation." Dual extraction is the standard for minimizing transcription errors.
• "You did not describe the data extraction form or pilot it." Piloting catches ambiguities in the form before full extraction begins.
• "How did you handle studies that reported medians and interquartile ranges instead of means and standard deviations?" Describe any conversion methods used (such as Wan et al., 2014 or Luo et al., 2018 estimators).

Study Risk of Bias Assessment: PRISMA 2020 Item 11

PRISMA 2020 Item 11 requires you to describe the methods used to assess the risk of bias in each included study, including the tool used, the domains assessed, and the number of reviewers who independently applied the tool. The Cochrane Handbook (Higgins et al., 2023) recommends RoB 2 for randomized trials and ROBINS-I for non-randomized studies.

What this subsection must contain:

• The specific risk of bias tool used, with a citation
• The domains assessed by that tool (for example, RoB 2 assesses randomization, deviations from intended interventions, missing outcome data, measurement of outcome, and selection of reported result)
• The number of reviewers who independently assessed each study
• How disagreements in risk of bias judgments were resolved
• Whether risk of bias assessments were used in sensitivity analyses or to judge the certainty of evidence

Example paragraph:

Common reviewer criticisms:

• "You used the Newcastle-Ottawa Scale for randomized trials. NOS is designed for observational studies." Match the tool to the study design.
• "Risk of bias was assessed by only one reviewer." Independent dual assessment is required.
• "You did not describe how risk of bias judgments informed your synthesis." Explain whether high-risk studies were excluded from sensitivity analyses or downgraded in certainty assessment.

Effect Measures: PRISMA 2020 Item 12

PRISMA 2020 Item 12 requires you to specify the effect measures used for each outcome (for example, risk ratio, odds ratio, mean difference, standardized mean difference, hazard ratio) and how they were selected.

What this subsection must contain:

• The primary effect measure for each outcome type (dichotomous, continuous, time-to-event)
• The rationale for choosing that measure
• Whether 95 percent confidence intervals were reported
• Any transformations applied (such as converting odds ratios to risk ratios, or using Hedges' g instead of Cohen's d for small samples)

Example paragraph:

Common reviewer criticisms:

• "Why did you use odds ratios when event rates exceed 20 percent? Odds ratios overestimate the effect in common outcomes." Justify the choice of effect measure relative to event frequency.
• "You did not specify whether you used Cohen's d or Hedges' g." Small-sample corrections matter; name the exact estimator.
• "Confidence intervals are missing for some outcomes." Always report both point estimates and intervals.

Struggling to draft a methods section that will satisfy peer reviewers? Research Gold's methodologists write and review methods sections for systematic reviews and meta-analyses across all clinical and social science disciplines. If you need expert feedback on your eligibility criteria, search strategy, or synthesis approach, get your project priced and tell us which sections you need help with. We also provide full Research Gold systematic review services from protocol to publication.

Synthesis Methods: PRISMA 2020 Item 13

PRISMA 2020 Item 13 is the most detailed methods item. It requires you to describe every step of your data synthesis, whether narrative or quantitative. If you conducted a meta-analysis, this section must cover the statistical model, the method for estimating heterogeneity, the software used, and any additional analyses (subgroup, sensitivity, meta-regression).

What this subsection must contain for a meta-analysis:

• Whether a fixed-effect or random-effects model was used, and why
• The heterogeneity estimator (DerSimonian-Laird, restricted maximum likelihood, Paule-Mandel, or another method)
• The heterogeneity statistics reported (Cochran's Q, I-squared, tau-squared, prediction interval)
• The statistical software and version (such as R version 4.3.2 with the metafor package, or Review Manager 5.4, or Stata 18)
• Subgroup analyses planned a priori, including the variables tested and the minimum number of studies required per subgroup
• Sensitivity analyses conducted (leave-one-out, exclusion of high risk of bias studies, fixed-effect vs. random-effects comparison)
• Whether publication bias was assessed (see Item 15)

What this subsection must contain for a narrative synthesis:

• The framework used for narrative synthesis (such as Synthesis Without Meta-analysis, or SWiM, reporting guidelines)
• How studies were grouped for narrative comparison
• How effect direction and magnitude were described across studies
• Whether vote counting or harvest plots were used

Example paragraph (meta-analysis):

Common reviewer criticisms:

• "You used DerSimonian-Laird but have fewer than 20 studies. REML or Paule-Mandel is more appropriate for small numbers of studies." The choice of heterogeneity estimator matters when the number of studies is small.
• "You reported I-squared but not the prediction interval. I-squared describes the proportion of variability, not the range of expected effects." Prediction intervals provide clinical context that I-squared alone cannot.
• "Your subgroup analyses were not pre-specified in the protocol." Post hoc subgroup analyses should be clearly labeled as exploratory.
• "You did not name the statistical software." Always report the software, version, and specific packages used.

Reporting Bias Assessment: PRISMA 2020 Item 15

PRISMA 2020 Item 15 requires you to describe the methods used to assess the risk of bias due to missing results in the synthesis (commonly called publication bias or reporting bias). This is distinct from the risk of bias within individual studies (Item 11).

What this subsection must contain:

• The methods used to assess publication bias (funnel plots, Egger's regression test, Begg's rank correlation test, or trim-and-fill analysis)
• The minimum number of studies required before these tests were applied (typically 10 studies for funnel plot-based methods)
• Whether selective reporting within studies was assessed (comparing published results with protocols or trial registrations)

Example paragraph:

Common reviewer criticisms:

• "You have only 6 studies in this meta-analysis. Funnel plots and Egger's test are unreliable with fewer than 10 studies." Acknowledge this limitation explicitly.
• "You did not assess selective reporting bias." Comparing published outcomes with protocol registrations is now expected under PRISMA 2020.
• "Your funnel plot shows asymmetry but you did not discuss it." Funnel plot asymmetry requires interpretation: it may indicate publication bias, small-study effects, or genuine heterogeneity.

Certainty Assessment: PRISMA 2020 Item 16

PRISMA 2020 Item 16 requires you to describe the methods used to assess the certainty (or quality) of the body of evidence for each outcome. The most widely used framework is GRADE (Grading of Recommendations, Assessment, Development and Evaluations), which rates certainty as high, moderate, low, or very low based on five domains.

What this subsection must contain:

• The framework used (GRADE, or an alternative if justified)
• The five GRADE domains assessed: risk of bias, inconsistency, indirectness, imprecision, and publication bias
• How certainty ratings were determined and by whom
• Whether summary of findings tables were produced (these are strongly recommended by Cochrane)

Example paragraph:

Common reviewer criticisms:

• "You did not use GRADE or any certainty assessment framework." Omitting certainty assessment is a major gap under PRISMA 2020.
• "Your GRADE ratings are inconsistent. You rated certainty as high despite serious risk of bias concerns." Each downgrading decision must be justified transparently.
• "You did not produce summary of findings tables." Cochrane and most high-impact journals now expect these tables.

How to Report Protocol Deviations

Nearly every systematic review deviates from its registered protocol in some way. PRISMA 2020 requires you to report all deviations transparently, explain why they occurred, and indicate whether they were made before or after data collection. The Cochrane Handbook (Higgins et al., 2023) emphasizes that unreported protocol deviations undermine the credibility of the entire review.

Common types of protocol deviations:

• Adding or removing outcomes after seeing the data
• Changing the eligibility criteria (for example, broadening the population definition because too few studies met the original criteria)
• Using a different risk of bias tool than originally planned
• Adding post hoc subgroup analyses that were not specified in the protocol
• Changing the statistical model (for example, switching from fixed-effect to random-effects after observing high heterogeneity)

How to report them:

Create a dedicated subsection titled "Deviations from the Registered Protocol" or include a table listing each deviation, the original plan, the change made, and the rationale. Reference your PROSPERO registration number so reviewers can verify the original protocol.

Example paragraph:

Register your protocol before starting your review using our free PROSPERO registration formatter, and consult our PROSPERO registration guide for step-by-step instructions.

How to Cite Tools and Software in Your Methods Section

Peer reviewers and journal editors expect you to cite every tool, software package, and guideline referenced in your methods section. Proper citation serves two purposes: it allows readers to replicate your methods, and it gives credit to tool developers whose work made your review possible.

Essential citations for a typical systematic review methods section:

Where to place citations: Cite each tool the first time you mention it in the methods section. Do not leave tool names uncited. If you used our free PRISMA visualization tool or build your search strategy, you can cite Research Gold alongside the relevant guideline.

PRISMA 2020 Methods Checklist: Items 5 through 16 at a Glance

Use this table as a final checklist before submitting your manuscript. Each row corresponds to a PRISMA 2020 methods item.

For a broader understanding of all 27 PRISMA 2020 items beyond the methods section, see our complete PRISMA 2020 guidelines explained.