BackgroundWith the failure of the latest vaccine trial, HVTN-505, HIV prevention efforts remain critical. Social and structural factors contributing to HIV and STI transmission include stigma regarding sexual violence, HIV infection and sexual orientation. For instance, HIV prevention and overall sexual health programs in Peru have been implemented yet key populations of youth (sex workers, male and transgender youth) continue to be overrepresented in new cases of HIV and STI. This suggests that interventions must take new directions and highlights the need for additional research.DiscussionWhile interdisciplinary, international research collaborations often are indicated as best practice in developing new knowledge in global health and an important component of the leadership in health systems, this does not mean they are free of challenges. In this debate we document our reflections on some of the challenges in developing an interdisciplinary and international research team to understand HIV and STI prevention priorities among youth in two culturally diverse cities in Peru: Lima, the capital city, and Ayacucho, in the Andean region.SummaryRather than offering solutions we aim to contribute to the debate about the object and purpose of global health research in the context of developing international research partnerships that genuinely promote a reciprocal and bidirectional flow of knowledge between the Global South and the Global North, and researchers at intersections of these locations.