The Cochrane Collaboration and the Joanna Briggs Institute are the two most widely cited sources of systematic review methodology in the biomedical and health sciences literature. They share foundational principles: both require pre-registered protocols, transparent and reproducible searching, systematic screening and critical appraisal, and structured reporting. They are not, however, the same methodology applied to the same questions.
JBI and Cochrane have different scopes, different critical appraisal tools, different approaches to certainty of evidence, and different review types they were each designed to support. Researchers who treat them as interchangeable references, or who mix guidance from both without explicitly documenting the integration, produce methods sections that do not hold together under peer review.
This guide covers the complete territory each organization owns, where they overlap, how their approaches to critical appraisal and GRADE differ, and a clear framework for deciding which methodology your review requires.
Quick Answer:
Cochrane primarily covers intervention reviews (effectiveness and safety of treatments, vaccines, devices, and procedures) and diagnostic test accuracy reviews. JBI covers a broader set of question types, including prevalence, etiology, qualitative evidence, text and opinion, mixed methods, and scoping reviews, in addition to effectiveness reviews. If your question is about the effectiveness of a healthcare intervention and your evidence base is primarily RCTs, both methodologies apply. If your question is about anything else, prevalence, patient experience, etiology, or qualitative evidence, JBI has the relevant methodology, and Cochrane does not.
What Each Organization Covers
The Cochrane Collaboration
The Cochrane Collaboration produces two primary methodological resources: the Cochrane Handbook for Systematic Reviews of Interventions (currently version 6.5, updated August 2024) and the Cochrane Handbook for Systematic Reviews of Diagnostic Test Accuracy. Cochrane's primary domain is the effectiveness and safety of healthcare interventions, with a strong emphasis on randomized controlled trials as the highest-quality evidence for intervention questions.
Cochrane reviews are characterized by a PICO-structured clinical question, mandatory registration on PROSPERO before screening begins, systematic searching of MEDLINE, EMBASE, and Cochrane CENTRAL as a minimum, dual independent screening and data extraction, risk-of-bias assessment using RoB 2 (for RCTs), ROBINS-I (for non-randomized intervention studies), or QUADAS-2 (for diagnostic accuracy studies), meta-analysis when studies are sufficiently homogeneous, GRADE certainty ratings, and reporting using PRISMA 2020.
The Cochrane Library publishes Cochrane Reviews, which undergo a formal editorial and peer review process governed by Cochrane's editorial policies. The Cochrane Handbook is also the methodological reference for many systematic reviews published outside the Cochrane Library in journals including BMJ, Lancet, Annals of Internal Medicine, and JAMA.
The Joanna Briggs Institute
JBI, based at the University of Adelaide, produces the JBI Manual for Evidence Synthesis. Unlike the Cochrane Handbook, which is organized around intervention and diagnostic question types, the JBI Manual is organized around the full range of evidence types that clinical, nursing, public health, and health policy research generates.
The JBI Manual covers the following review types:
Systematic reviews of effectiveness (equivalent in scope to Cochrane intervention reviews). Systematic reviews of prevalence and incidence. Systematic reviews of etiology and risk. Systematic reviews of diagnostic test accuracy. Systematic reviews of qualitative evidence. Systematic reviews of text and opinion. Mixed-methods systematic reviews. Scoping reviews. Umbrella reviews. Economic evidence syntheses.
JBI also publishes its own critical appraisal checklists for each study design it covers, which differ from the Cochrane tools in structure and in the outcomes they assess. For certainty of evidence, JBI uses GRADE for quantitative effectiveness reviews and the ConQual tool for qualitative evidence syntheses, rather than applying standard GRADE to all evidence types.
JBI Evidence Synthesis is the organization's primary journal, and JBI-affiliated review groups operate across multiple countries with structured training and review support.
Head-to-Head Comparison by Review Type
The simplest way to understand which methodology applies to your review is to identify your question type and match it to the appropriate organizational domain.
Effectiveness of a healthcare intervention: Both Cochrane and JBI cover this question type. If your institution has Cochrane review infrastructure or your target journal is the Cochrane Database of Systematic Reviews, use the Cochrane Handbook. If your institution has JBI review infrastructure or your target journal is JBI Evidence Synthesis, use the JBI Manual for effectiveness reviews. If you are publishing in a general clinical journal, either methodology is acceptable, but your methods section must be internally consistent with whichever you choose.
Diagnostic test accuracy: Cochrane has a dedicated handbook for DTA reviews. JBI also provides guidance for DTA reviews. The Cochrane DTA handbook is the more detailed and widely cited resource. Either can be used, but the Cochrane handbook is the standard reference for DTA reviews submitted to major clinical journals.
Prevalence and incidence of a condition: JBI. The Cochrane Handbook does not cover prevalence or incidence reviews. A methods section for a prevalence review that cites the Cochrane Handbook as its methodological foundation is missing the relevant framework. JBI's critical appraisal checklist for prevalence and incidence studies, the JBI MAStARI instrument, is the appropriate tool for this question type.
Etiology and risk factors: JBI. Questions about what factors are associated with the development or progression of a condition use cohort and case-control study designs that fall within JBI's etiology review scope. JBI's critical appraisal checklist for cohort studies and case-control studies provides the appropriate appraisal framework.
Patients' experiences, perspectives, or the meaning of a phenomenon: JBI qualitative evidence synthesis. This question type requires qualitative study designs, phenomenology, grounded theory, ethnography, and similar approaches, that the Cochrane Handbook was not designed to address. JBI's qualitative synthesis methodology, including the ConQual confidence assessment tool, is the appropriate framework.
Text and opinion: JBI. This review type synthesizes evidence from expert opinion papers, policy documents, and clinical guidelines. It is relevant for questions in areas where primary research is sparse but professional consensus and policy guidance exist. Cochrane does not have a corresponding review type.
Scoping reviews: Both JBI and Cochrane provide scoping review guidance, but they differ significantly. JBI's scoping review method follows the Arksey and O'Malley framework updated by Peters and colleagues, uses a JBI-specific protocol template, and follows PRISMA-ScR for reporting. Cochrane's guidance on scoping reviews is less prescriptive and primarily directed at scoping reviews conducted as a precursor to intervention systematic reviews. For a formal scoping review submitted to JBI Evidence Synthesis, use the JBI method.
Mixed-methods reviews: JBI. The JBI Manual provides detailed guidance on convergent and sequential integration designs for mixed-methods systematic reviews. The Cochrane Handbook does not currently provide a complete mixed-methods review methodology.
Umbrella reviews: Both organizations provide some guidance, but neither provides a complete and widely adopted standard. The PRIOR (Preferred Reporting Items for Overviews of Reviews) reporting guideline applies to umbrella reviews regardless of the primary systematic review methodology used.
Critical Appraisal Tools
The critical appraisal tools used in JBI and Cochrane reviews differ by design and by the study types they cover.
Cochrane tools:
RoB 2 (Cochrane Risk of Bias Tool for Randomized Trials, Sterne et al., BMJ 2019): five domains covering randomization, deviations from intended interventions, missing outcome data, measurement of the outcome, and selection of the reported result.
ROBINS-I (Risk of Bias in Non-randomized Studies of Interventions, Sterne et al., BMJ 2016): seven domains for observational studies of interventions.
QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies 2, Whiting et al., Ann Intern Med 2011): four domains for diagnostic accuracy studies.
JBI tools:
JBI has developed critical appraisal checklists for a wider range of study designs than Cochrane, reflecting the broader scope of evidence types it covers. These include checklists for randomized controlled trials, quasi-experimental studies, cohort studies, case-control studies, analytical cross-sectional studies, prevalence studies, case series, case reports, qualitative research, text and opinion papers, economic evaluations, and diagnostic test accuracy studies.
JBI's checklists use a simpler yes/no/unclear/not applicable scoring format rather than the domain-level judgment structure of Cochrane's tools. This makes them faster to apply but has been associated with lower inter-rater reliability in some study comparisons.
For qualitative evidence syntheses, JBI uses the ConQual tool to assess confidence in qualitative findings. ConQual operates on two dimensions, dependability (the quality of the qualitative research methods) and credibility (the extent to which the findings are supported by the data), and produces a confidence rating of high, moderate, low, or very low. This is distinct from standard GRADE, which was developed for quantitative evidence, and its application to qualitative research is explicitly recommended in the JBI Manual rather than as a workaround.
How GRADE Differs Between JBI and Cochrane
Both JBI and Cochrane use GRADE for quantitative effectiveness reviews, and their application of the five downgrading domains (risk of bias, inconsistency, indirectness, imprecision, and publication bias) is consistent with the GRADE Working Group's guidance.
The difference is in how each organization handles the certainty of evidence for non-quantitative review types.
Cochrane does not provide a complete GRADE framework for qualitative evidence. The Cochrane Qualitative and Implementation Methods Group has published discussions of applying qualitative evidence in GRADE assessments, but this is an evolving area rather than a settled methodology.
JBI addresses this explicitly by recommending ConQual for qualitative evidence syntheses rather than standard GRADE. For mixed-methods reviews, JBI recommends integrating ConQual ratings from the qualitative component with GRADE ratings from the quantitative component, using a convergent integrated design.
Applying standard GRADE to qualitative evidence, as some research teams do when they have GRADE expertise but have not read the JBI guidance for their review type, produces certainty ratings that are methodologically inconsistent with the evidence type they are being applied to. This is a specific issue that peer reviewers at JBI Evidence Synthesis and methodology-focused journals will identify and flag.
For a deeper understanding of how PRISMA 2020 interacts with both methodologies at the reporting stage, our complete PRISMA 2020 checklist guide covers every reporting item with the most common failures.
A Decision Framework for Choosing Your Methodology
The following five questions lead to a clear methodology choice for most systematic reviews.
Question 1: What is my primary question type? Effectiveness of an intervention: either Cochrane or JBI. Diagnostic accuracy: Cochrane DTA handbook or JBI. Prevalence, incidence, etiology: JBI. Qualitative evidence, text, and opinion: JBI. Mixed methods: JBI. Scoping review: JBI (for a formal JBI scoping review) or either (for a general scoping review).
Question 2: What study designs does my evidence base include? Primarily RCTs: Cochrane is the primary reference. Non-randomized studies, observational designs, qualitative studies, policy documents: JBI has the appropriate tools.
Question 3: What is my target journal? Cochrane Database of Systematic Reviews: Cochrane methodology. JBI Evidence Synthesis: JBI methodology. General clinical journals (BMJ, Lancet, JAMA, Annals): either, but the methods section must be internally consistent. Nursing, public health, or allied health journals: JBI is frequently the more appropriate reference given the question types common in these fields.
Question 4: What is my institution's review infrastructure? Cochrane review groups and affiliated centers provide training and support for Cochrane reviews. JBI Collaborating Centers provide training and support for JBI reviews. Institutional affiliation often determines which support is accessible and which methodology the team is trained in.
Question 5: Am I able to commit to one methodology consistently? The answer to this question determines how you write your methods section. A methods section must cite the relevant sections of the chosen manual specifically, not both manuals generally. "We followed the Cochrane Handbook (Higgins et al., 2024) and the JBI Manual (JBI, 2020)" without specifying which guidance was followed for which methodological decision is not an adequate methods description.
For guidance on what question type and review design your specific research question calls for, our guide to types of systematic review and which one your question requires covers the full decision process.
Common Errors in JBI and Cochrane Method Reporting
The most consistent errors that peer reviewers flag in methods sections that cite JBI or Cochrane guidance fall into three categories.
Citing both without specifying which: As described throughout this guide, citing both the Cochrane Handbook and the JBI Manual as co-equal methodological references without specifying which was followed for which decision is the most common error. The fix is to choose one primary framework and cite specific chapters and sections.
Using Cochrane tools for non-Cochrane question types: Applying RoB 2 to a prevalence study, or applying GRADE to qualitative evidence without ConQual, are tool-selection errors that indicate the team used familiar tools rather than the tools appropriate to their question type.
Registering a JBI review on PROSPERO with a Cochrane protocol structure: PROSPERO accepts registrations for all systematic review types, but the protocol elements that reviewers expect to see vary by methodology. A JBI qualitative evidence synthesis registered with a protocol structured around a PICO question and RCT eligibility criteria has a protocol-methodology mismatch.
Understanding these errors in the context of how they affect publication outcomes is covered in our guide to why systematic reviews get rejected before peer review.
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Frequently Asked Questions
Can I switch from Cochrane to JBI methodology after registration?
Changing methodology after PROSPERO registration is a protocol deviation that must be documented and justified in the manuscript. If the question type actually requires JBI methodology and the protocol was registered with Cochrane methodology, the amendment should be registered on PROSPERO with an explanation and should be transparently reported in the published methods section. Peer reviewers and editors will see the original registration and the deviation.
Which methodology produces higher-quality reviews?
Neither methodology is inherently superior. Quality depends on the alignment between the question type, the methodology, the tools applied, and the rigor of execution. A JBI qualitative evidence synthesis conducted to JBI standards is not of lower quality than a Cochrane intervention review conducted to Cochrane standards. Quality comparisons across methodologies are only meaningful when the same question type is compared using each methodology's appropriate tools.
Does Cochrane cover qualitative research?
The Cochrane Handbook and the Cochrane Qualitative and Implementation Methods Group provide some guidance on incorporating qualitative evidence into evidence synthesis, particularly through the GRADE-CERQual approach for integrating qualitative findings into Summary of Findings tables. However, the Cochrane Handbook does not provide a complete standalone methodology for qualitative evidence synthesis in the same way the JBI Manual does. For a primary qualitative evidence synthesis, JBI is the more complete methodological reference.
Is the JBI Manual publicly available?
Yes. The JBI Manual for Evidence Synthesis is freely available at jbi.global/resources/synthesis-resources. Cochrane's training resources and the Cochrane Handbook are available at training.cochrane.org.
Do I need Cochrane affiliation to follow Cochrane methodology?
No. The Cochrane Handbook is a publicly available methodological resource that any research team can follow. Cochrane affiliation is required to publish in the Cochrane Database of Systematic Reviews, but not to conduct a systematic review following Cochrane methodology for publication in any other journal.
