The aim of this study is to estimate the prevalence of HIV/HBV and HIV/HCV coinfections among AIDS cases reported in Brazil, and to describe the epidemiological profile of these cases. Coinfection was identified through probabilistic record linkage of the data of all patients carrying the HIV virus recorded as AIDS patients and of those patients reported as carriers of hepatitis B or C virus in various databases from the Brazilian Ministry of Health from 1999 to 2010. In this period 370,672 AIDS cases were reported, of which 3,724 were HIV/HBV coinfections. Women are less likely to become coinfected than men and the chance of coinfection increases with age. This study allowed an important evaluation of HBV/HIV and HCV/HIV coinfections in Brazil using information obtained via merging secondary databases from the Ministry of Health, without conducting seroprevalence research. The findings of this study might be important for planning activities of the Brazilian epidemiologic surveillance agencies.