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Research capacity strengthening (RCS) in health social science research is considered a key imperative to achieve health equity. Recent evidence suggests that the knowledge gap between the North and the South, particularly low income developing countries, is growing ever wider in spite of the prominence capacity development and RCS enjoy in development assistance policy. This paper addresses this concern by analyzing the political economy of the prevailing modes of research commissioning among bilateral, multilateral, non-governmental and philanthropic organizations in East Africa (Uganda, Kenya and Tanzania). In doing so the paper shifts the lens from the conventional focus on recipient countries and institutions to look at the policies and practices of donor and commissioning agencies and the relationship they have with key stakeholders like Southern research institutions. The research shows that the thinking on RCS has shifted towards partnership models but that this has generally not been translated into policy and action among most commissioning and donor agencies in the field. It can also be argued that the literatur