BACKGROUND: The effects of HIV and antiretroviral therapy on cardiovascular system of perinatally infected children throughout their development are not fully understood. OBJECTIVES: To determine the prevalence of cardiac abnormalities in a retrospective cohort of perinatally HIV-infected patients and to investigate associations between echocardiographic and clinical data during their follow-up. METHODS: Review of medical records and echocardiogram reports of 148 perinatally HIV-infected patients between January 1991 and December 2015. RESULTS: Four hundred and eighty echocardiograms were analyzed and 46 (31%) patients showed cardiac abnormalities, frequently subclinical and transient. Nadir CD4 count was higher in patients with consistently normal echocardiogram: 263 (4-1480) versus 202 (5-1746) cells/µL, P = 0.021. Right ventricular (RV) dilation was detected in 18.9%, left ventricular (LV) dilation in 21.6%, septal hypertrophy in 12.2%, LV posterior wall hypertrophy in 6%, LV systolic dysfunction in 8% and pulmonary hypertension in 8.7% of patients. Opportunistic infections were associated with RV dilation [odds ratio (OR = 4.34; 1.78-10.53; P < 0.01)], pulmonary hypertension (OR = 8.78; 2.80-27.51; P < 0.01) and LV systolic dysfunction (OR = 5.38; 1.55-18.71; P < 0.01). Longer duration of highly active antiretroviral therapy was associated with reduced risk of LV dilation (OR = 0.91; 0.85-0.97; P < 0.01) and systolic dysfunction (OR = 0.71; 0.59-0.85; P < 0.01). Protease inhibitors use was associated with reduced risk of RV dilation (OR = 0.54; 0.30-0.97; P < 0.05), LV dilation (OR = 0.35; 0.21-0.60; P < 0.01) and LV systolic dysfunction (OR = 0.07; 0.02-0.31; P < 0.01). Higher CD4 count was associated with lower risk of LV systolic dysfunction (OR = 0.82; 0.69-0.98; P < 0.05). CONCLUSIONS: Echocardiograms identified cardiac abnormalities among children with perinatally acquired HIV infection, and data suggest that immunologic status and therapeutic strategies throughout development can influence cardiac disease burden in this population.