Virologic factors may influence survival of HIV-1-infected infants. We compared survival of Ugandan infants with subtype A and subtype D HIV-1 infection. This study was performed in the context of the Ugandan clinical trial HIVNET 012, which compared the efficacy of single-dose nevirapine (NVP) and short-course zidovudine (AZT) for prevention of HIV-1 mother-to-child transmission. HIV-1 subtypes were determined by phylogenetic analysis of HIV-1 protease and reverse transcriptase sequences from 32 women in the NVP arm and 54 women in the AZT arm of HIVNET 012 whose infants were HIV-1 infected by 6 to 8 weeks of age. We found no association between HIV-1 subtype (A vs. D) and infant survival in this cohort. Further studies are needed to evaluate whether HIV-1 subtype influences clinical outcome in pediatric HIV-1 infection.