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Recent scholarship has considered what, if anything, rich people owe to poor people to achieve justice in global health and the implications of this for international research. Yet this work has primarily focused on international clinical research. Health systems research is increasingly being performed in low and middle income countries and is essential to reducing global health disparities. This paper provides an initial description of the ethical issues related to priority setting, capacity-building, and the provision of post-study benefits that arise during the conduct of such research. It presents a selection of issues discussed in the health systems research literature and argues that they constitute ethical concerns based on their being inconsistent with a particular theory of global justice (the health capability paradigm). Issues identified include the fact that priority setting for health systems research at the global level is often not driven by national priorities and that capacity-building efforts frequently utilize one-size-fits-all approaches.