The role of non-tuberculous mycobacteriosis (NTM) in HIV-related diseases in sub-Saharan Africa has long been controversial. In a 6-year cohort of 721 HIV-infected adults with systematic BACTEC blood cultures in Abidjan, Côte d'Ivoire, the incidence of NTM was 1.8/100 person-years overall and 12.2/100 person-years in patients with baseline CD4 cell counts < 100 cells/mm3. In sub-Saharan Africa, where most patients start highly active antiretroviral therapy with low CD4 cell counts, improving the diagnosis of NTM may be relevant.