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There is geographical overlap between areas endemic for rheumatic heart disease (RHD) and those endemic for HIV. A recent pilot study demonstrated that children living with HIV might be at less risk for RHD development; however, the sample size was too small to make definitive conclusions. Our objective was to determine the prevalence of RHD among HIV-positive children in Uganda.We conducted a prospective, cross-sectional study of HIV-positive children (5–15 years of age) receiving care at the Baylor Uganda HIV Clinic, Kampala, Uganda. A focused echocardiogram and chart review was performed. A sample size of 988 children was needed to provide 80% power to detect a difference in population prevalence between HIV-positive children and the general population, 2.97% [95% confidence interval (CI): 2.70–3.24%], based on previous reports.Screening echocardiography of 993 HIV-positive children found 15 individuals (1.5%; 95% CI: 0.88%–2.54%) with RHD. Of these 15, 2 were classified as definite RHD and 13 as borderline RHD. The majority of children had isolated mitral valve disease (93%). Children found to have RHD were older than those without RHD, 12 versus 10 years of age (P = 0.004). When separated based on geographic location, the prevalence of RHD among HIV-positive children from Kampala was 1.28% (95% CI: 0.63%–2.51%) compared with 2.1% (95% CI: 0.89%–4.89%) in those from outside Kampala.Children living with HIV have a lower prevalence of RHD than the general pediatric population. Further studies are needed to explore this protective association.