Researchers studying health systems in low-income countries face a myriad of ethical challenges throughout the entire research process. In this article, we discuss one of the greatest ethical challenges that we encountered during our fieldwork in West Africa: the difficulty of protecting the confidentiality of participants while locally disseminating results of health systems research to stakeholders. This reflection is based on experiences of authors involved in conducting evaluative research of interventions aimed at improving health systems in West Africa. Our observation (...) and collaboration with the research projects’ stakeholders informed our analysis. Examples from two research projects illustrate the issues raised. We found that in some cases there is a risk that local stakeholders may be able to identify research participants, or at least groups of participants, during the dissemination of results, even if they are anonymized. Four factors can interact and influence this challenge: 1) hierarchical structure, 2) small milieu, 3) immersion in a few sites, and 4) vested interests of decision-makers. For example, local stakeholders can sometimes find out when and where the data were collected. Moreover, health systems, especially rural healthcare centres, in West African countries can be small settings, so people often know each other. Some types of participants have unique characteristics or positions in the health system that may make them more easily identifiable by local stakeholders familiar with the environment. We identified a number of potential strategies that can help researchers minimize this difficulty and improve ethical research practices. These strategies pertain to the development of the study design, the process of obtaining informed consent, the dissemination of results, and the researchers’ reflexivity. Researchers must develop and adopt strategies that enable them to respect their promise of confidentiality while effectively disseminating sometimes sensitive results. Reflections surrounding ethical issues in global health research should be deepened to better address how to manage competing ethical responsibilities while promoting valuable research uptake. (shrink)