Interuniversity global health partnerships are often between parties unequal in organizational capacity and performance using conventional academic output measures. Mutual benefit and reciprocity are called for but literature examining these concepts is limited. The objectives of this study are to analyse how reciprocity is practiced in international interuniversity global health partnerships and to identify relevant structures of reciprocity. Four East African universities and 125 of their international partnerships were included. A total of 192 representatives participated in key informant interviews and focus group discussions. Interviews were transcribed and analysed thematically, drawing on reciprocity theories from international relations and sociology. A range of reciprocal exchanges, including specific, unilateral and diffuse (bilateral and multilateral), were observed. Many partnerships violated the principle of equivalence, as exchanges were often not equal based on tangible benefits realized. Only when intangible benefits, like values, were considered was equivalence realized. This changed the way the principle of contingency--an action done for benefit received--was observed within the partnerships. The values of individuals, the structures of organizations and the guiding principles of the partnerships were observed to guide more than financial gain. Asymmetry of partners, dissimilar perspectives and priorities, and terms of funding all pose challenges to reciprocity. In an era when strengthening institutions is considered crucial to achieving development goals, more rigorous examination and assessment of reciprocity in partnerships is warranted.