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Introduction Health reporting is one of the foundations on which public health interventions and policies as well as prevention measures are developed. However, it faces the challenge of adequately reflecting social and sex/gender-related heterogeneity. The German Federal Ministry of Education and Research-funded joint project, AdvanceGender, aims to develop guidelines for sex/gender-sensitive and intersectional approach to population-based studies and health reporting. In its subproject, AdvanceHealthReport, four focus groups will be conducted to provide essential information on possible ways of participation of civil society stakeholders and on communication of health information for the further development of the guidelines (research period: from January 2019 to March 2020).Methods and analysis The civil society stakeholders provide valuable information which health topics are relevant in regard to specific populations and how health information should be communicated in a non-stigmatising way. The groups will also discuss how civil society stakeholders should participate in health reporting. The starting point for intersections will be sex/gender. The intersection of sex/gender and migration and sex/gender and sexual orientation is particularly taken into account. The focus groups will be recorded, transcribed, anonymised and then analysed according to the qualitative content analysis.Results The results will show the pathways as well as benefits and possible limitations of civil society stakeholder involvement in national health reporting and will contribute in developing guidelines for sex/gender-sensitive and intersectional health reporting.Ethics and Dissemination The results of the focus groups will be published in scientific journals and presented at various national and international conferences. Furthermore, the findings will be incorporated into guidelines for research and health reporting. The study was approved by the Ethics Commission of Brandenburg Medical School Theodor Fontane (AZ: E-01–20180529).