Health research priority setting processes assist researchers and policymakers in effectively targeting research that has the greatest potential public health benefit. Many different approaches to health research prioritization exist, but there is no agreement on what might constitute best practice. Moreover, because of the many different contexts for which priorities can be set, attempting to produce one best practice is in fact not appropriate, as the optimal approach varies per exercise. Therefore, following a literature review and an analysis of health research priority setting exercises that were organized or coordinated by the World Health Organization since 2005, we propose a checklist for health research priority setting that allows for informed choices on different approaches and outlines nine common themes of good practice. It is intended to provide generic assistance for planning health research prioritization processes. The checklist explains what needs to be clarified in order to establish the context for which priorities are set; it reviews available approaches to health research priority setting; it offers discussions on stakeholder participation and information gathering; it sets out options for use of criteria and different methods for deciding upon priorities; and it emphasizes the importance of well-planned implementation, evaluation and transparency.