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Background: In-country research capacity is key to creating improvements in local implementation of health programs and can help prioritize health issues in a landscape of limited funding. Research prioritization has shown to be particularly useful to help answer strategic and programmatic issues in health care, including sexual and reproductive health (SRH). The purpose of this paper is to present the results of a priority setting exercise that brought together researchers and program managers from the WHO Africa and Eastern Mediterranean regions to identify key SRH issues. Methods: In June 2015, researchers and program managers from the WHO Africa and Eastern Mediterranean regions met for a three-day meeting to discuss strategies to strengthen research capacity in the regions. A prioritization exercise was carried out to identify key priority areas for research in SRH. The process included five criteria: answerability, effectiveness, deliverability and acceptability, potential impact of the intervention/program to improve reproductive, maternal and newborn health substantially, and equity. Results: The six main priorities identified include: creation and investment in multipurpose prevention technologies, addressing adolescent violence and early pregnancy (especially in the context of early marriage), improved maternal and newborn emergency care, increased evaluation and improvement of adolescent health interventions including contraception, further focus on family planning uptake and barriers, and improving care for mothers and children during childbirth. Conclusion: The setting of priorities is the first step in a dynamic process to identify where research funding should be focused to maximize health benefits. The key elements identified in this exercise provides guidance for decision makers to focus action on identified research priorities and goals. Prioritization and identifying/acting on research gaps can have great impact across multiple sectors in the regions for improved reproductive, maternal and children health. [ABSTRACT FROM AUTHOR]