In order to determine the rate and the different causes of mortality associated with HIV/AIDS in health-care facilities we conducted a prospective study between 1 April and 30 September 2010 in the six health regions of Togo. We rationalized the choice of the healthcare facilities in order to cover the entire national territory. During the study period, 24,054 patients were hospitalized. HIV serology was positive in 1065 (18.2%) of the 5865 tested patients. Of the 24,054 patients, we recorded 2551 deaths (10.6%), including 309 HIV-infected patients (5.2%). The mortality rate associated with HIV/AIDS was 1.3% of the total number of inpatients and 5.3% of the number of patients tested for HIV. The mortality rate among HIV-infected patients was 29%. The causes of death in patients infected with HIV/AIDS were mainly anaemia and cerebral toxoplasmosis. This study shows that mortality associated with HIV/AIDS in health-care facilities in Togo remains relatively high.