The selection of appropriate outcomes is crucial when designing clinical trials in order to compare the effects of different interventions directly. For the findings to influence policy and practice, the outcomes need to be relevant and important to key stakeholders including patients and the public, health care professionals and others making decisions about health care. It is now widely acknowledged that insufficient attention has been paid to the choice of outcomes measured in clinical trials. Researchers are increasingly addressing this issue through the development and use of a core outcome set, an agreed standardised collection of outcomes which should be measured and reported, as a minimum, in all trials for a specific clinical area.Accumulating work in this area has identified the need for guidance on the development, implementation, evaluation and updating of core outcome sets. This Handbook, developed by the COMET Initiative, brings together current thinking and methodological research regarding those issues. We recommend a four-step process to develop a core outcome set. The aim is to update the contents of the Handbook as further research is identified.Electronic supplementary materialThe online version of this article (doi:10.1186/s13063-017-1978-4) contains supplementary material, which is available to authorized users.

We identify a number of procedural, conceptual and theoretical issues that need to be addressed in moving forward with this area, and emphasise the need for existing techniques to be evaluated and modified, rather than inventing new approaches.

Systematic review has developed as a specific methodology for searching for, appraising and synthesizing findings of primary studies, and has rapidly become a cornerstone of the evidence-based practice and policy movement. Qualitative research has traditionally been excluded from systematic reviews, and much effort is now being invested in resolving the daunting methodological and epistemological challenges associated with trying to move towards more inclusive forms of review. We describe our experiences, as a very diverse multidisciplinary group, in attempting to incorporate qualitative research in a systematic review of support for breastfeeding. We show how every stage of the review process, from asking the review question through to searching for and sampling the evidence, appraising the evidence and producing a synthesis, provoked profound questions about whether a review that includes qualitative research can remain consistent with the frame offered by current systematic review methodology. We conclude that more debate and dialogue between the different communities that wish to develop review methodology is needed, and that attempts to impose dominant views about the appropriate means of conducting reviews of qualitative research should be resisted so that innovation can be fostered.

We identify a number of procedural, conceptual and theoretical issues that need to be addressed in moving forward with this area, and emphasise the need for existing techniques to be evaluated and modified, rather than inventing new approaches.

Structured approaches may not produce greater consistency of judgements about whether to include qualitative papers in a systematic review. Future research should address how appraisals of qualitative research should be incorporated in systematic reviews.