Pregnancies in women without knowledge of their HIV-positive status increase the risk of mother-to-child transmission, and of disease progression. This study aimed to characterize the frequency of multiple pregnancies and of HIV-positive children in the family, during HAART era. We analyzed data of a national multicenter cohort study among Brazilian children with AIDS diagnosed between 1999 and 2002. In total, 945 children and their 928 mothers were included. Five hundred and ninety (64.6%) women had a history of multiple pregnancies, and 49.5% attended prenatal care (mean: 3.5 consultations; SD 3.6). In 483 child cases, HIV status of the sibling was known; 130 (26.9%) of these were infected with HIV. In 38.5% of cases, the child with AIDS included in the cohort study was the first case in the family. Despite the overall positive results of the Brazilian control policy of HIV/AIDS, our study shows that HIV infection in pregnant women was often undetected and that consequently there was a high frequency of repeated HIV-infected children. There is a need to improve comprehensive prenatal and postnatal care of Brazilian women. HIV-affected families are most vulnerable and should be targeted by specific control programs, preventing additional HIV infections in other children.