The Bissau HIV Cohort aims to investigate the efficacy of antiretroviral therapies in populations infected with multiple types of HIV. It was established in July 2007 by the Bandim Health Project (BHP) and Aarhus University Hospital, Denmark, in collaboration with nurses and physicians from the Hospital Nacional Simão Mendes in Guinea-Bissau. All HIV-positive patients presenting at the HIV clinic at Hospital Nacional Simão Mendes are invited to be enrolled in the cohort. Patients are referred to the clinic from the hospital wards, health centres, and the hospital’s blood bank. From July 2007 to June 2013, more than 3,700 patients attending the clinic were included in the cohort. For patients on antiretroviral therapy, visits are initially monthly, then every 2–3 months as therapy stabilises. Patients who are not on antiretroviral therapy are seen approximately every 6 months.