Renal toxicity is a concern in HIV-infected children receiving antiretrovirals. However, the prevalence [1.7%; 95% confidence interval (CI): 1.0-2.6%] and incidence of kidney dysfunction (0.17 cases/100 person-years; 95% CI: 0.04-0.30) were rare in this multicenter cohort study of 1,032 perinatally HIV-infected Latin American and Caribbean children followed from 2002 to 2011.