Minority population groups are often excluded or marginalised within health systems and in health research and policy. This article argues that theories of intersectionality can help us to understand these issues and develops the concept of 'hidden healthcare populations' - using the case of people who identify as Lesbian, Gay, Bisexual, Transgender Plus (LGBT+) in Nigeria, in sub-Saharan Africa. The findings present original qualitative data from a seldom heard population group about instances of abuse, rejection and marginalisation by healthcare providers working in public and private healthcare facilities, and the attempts of LGBT+ people to resist and survive in that context. We extend theoretical understandings of intersectionality in global public health and explore how the concept relates to the social determinants of health. The article has significant implications for policy and healthcare education and responds to a call from the World Health Organisation to generate context-specific data to guide interventions targeted at minority population groups. Additionally, our discussion has wider significance because it highlights the Western-centric nature of much theory in health policy - and offers analysis and reinterpretation that incorporates queer, postcolonial, African perspectives.