Objectives Dyslipidemia is common in HIV-infected children, due to the infection itself and the anti-retroviral drugs, particularly protease-inhibitors. We aimed to study the prevalence of dyslipidemia and its association with diet and physical activity in children in anti-retroviral treatment in El Salvador. Materials and Methods We surveyed 270 children aged 5-18 years in anti-retroviral therapy at a reference centre of El Salvador. Anthropometric measures were obtained and information gathered on socio-demographic characteristics, type and length of therapy, diet and physical activity. Triglycerides, total cholesterol, low-density lipoprotein (LDL), high-density lipoprotein (HDL), viral load, and CD4 concentration were measured. Abnormal lipid concentrations were defined as triglycerides ≥130 mg/dl in children aged 10-19 years and ≥100 mg/dl in < 10 years; total cholesterol ≥200 mg/dl, LDL ≥130 mg/dl and HDL ≤35 mg/dl. Dietary patterns were identified by principal component analysis and the “high fat/sugar diet” pattern was used as a proxy of unhealthy diet. We performed a descriptive analysis by sex, and adjusted four logistic multivariate models to assess the association of each type of dyslipidemia with diet and physical exercise. Results Of the 270 children – 80 of whom taking protease-inhibitors - 128 (47.4%) had high triglycerides and 36 (13.3%) high total cholesterol concentrations. High LDL were observed in 17/176 children (9.7%) and low HDL in 39/183 (21.3%). No difference by sex were found in the lipids profile nor in the adherence to the unhealthy diet, but significantly more boys than girls were doing exercise at least three times a week (81.4% versus 59.2%, p