BACKGROUND There are very few published studies of heart disease in HIV infected children living in sub-Saharan Africa, a region with more than 50% of the world's population of HIV infected patients. OBJECTIVE To determine the prevalence, and describe the type and clinical presentation of heart disease among children with HIV attending an ambulatory clinic. METHODS Two hundred and thirty (230) HIV infected children attending the Paediatric Infectious Disease Clinic at Mulago hospital were recruited by simple random sampling in a cross-sectional study. The children were evaluated clinically, and investigated by electrocardiography and echocardiography. RESULTS Thirty-two children (13.9%) had asymptomatic HIV disease, 156 (67.8%) had AIDS related complex while 42 (18.3%) had AIDS. Heart abnormalities were detected in 51% of the children (40.0% by echocardiography alone and 26.5% by electrocardiography alone). Heart abnormalities were most prevalent in children with AIDS (76.2%) and least prevalent in children with asymptomatic HIV disease (25.0%). The abnormalities included; Sinus tachycardia (21%), left ventricular systolic dysfunction (17%), right ventricular dilatation (14%), congenital heart disease (4.8%), dilated cardiomyopathy (3.0%), pericarditis (2.2%) and cor pulmonale (1.3%). Children with left ventricular systolic dysfunction significantly had easy fatigability, dyspnoea on exertion and tachypnoea. Other heart abnormalities presented with non-specific clinical features. CONCLUSIONS Heart abnormalities were common especially in children with symptomatic HIV disease and included sinus tachycardia, left ventricular systolic dysfunction and right ventricular dilatation. The detected heart abnormalities, except left ventricular systolic dysfunction, had non-specific clinical features.