We set out to investigate whether there are clinically significant consequences when children with perinatal exposure to single-dose nevirapine are initiated on a nonnucleoside reverse transcriptase inhibitor (NNRTI) containing a highly active antiretroviral therapy (HAART) regimen. We carried out a chart and database review of 104 HIV-infected children, who had initiated HAART with an NNRTI at JCRC and were less than or equal to 5 years of age, 35 (33.7%) of whom had prior exposure to perinatal single-dose nevirapine. We studied the viral load and CD4 percentage at baseline, at week 24, and at week 48 after the start of HAART in children exposed and not exposed to perinatal single-dose nevirapine, as well as the results of genotypic resistance testing done for the children who had failed to achieve virologic suppression on HAART. At weeks 24 and 48 after initiating HAART, children not exposed to single-dose nevirapine were 3.28 times [OR = 3.28, 95% CI: (1.37 to 9.20), p = 0.0167] and 3.47 times [OR = 3.47, 95% CI: (1.28 to 9.37), p = 0.0091] more likely to achieve virologic suppression compared to children exposed to single-dose nevirapine, respectively. However, the CD4 cell response at weeks 24 and 48 was not worse in the children exposed to single-dose nevirapine. In 10 children with perinatal exposure to single-dose nevirapine, NNRTI resistance mutations, mostly K103N, Y181C, and G109A, were identified. HIV-infected children with perinatal exposure to single-dose nevirapine are less likely to achieve short-term virologic suppression when started on an NNRTI-containing regimen, when compared to those who were not exposed to it, probably because the exposure predisposes them to developing NNRTI resistance mutations.