We measured virologic suppression among 34 nevirapine (NVP)-exposed HIV-infected children with median age of 8.6 months (range: 3.2-19.9) initiating NVP-based antiretroviral therapy (ART) in rural Uganda. In Kaplan-Meier analysis, the cumulative probability of virologic suppression, defined as having two consecutive HIV-1 RNA <400 copies ml(-1) by 18 months was 56%. In multivariate Cox proportional hazard modeling, the following pre-ART measurements were independently associated with an increased probability of viral suppression: increasing age [hazard ratio (HR) =1.28 per 1 month increase in age, p = 0.002], lower viral load (HR = 3.54 for HIV RNA > 7 50 000 copies ml(-1), p = 0.03) and high CD4% (HR = 6.0 for CD4% > 25, p = 0.003). These results lend additional support to the 2010 World Health Organization recommendations that protease inhibitors be used to treat NVP-exposed children, but that NVP-based ART should be initiated before the decline of CD4% to optimize outcomes in NVP-exposed children when protease inhibitors are not available.