The aim of present study was to describe the frequency of lipodystrophy syndrome associated with HIV (LSHIV) and factors associated with dyslipidemia in Brazilian HIV infected children. HIV infected children on antiretroviral treatment were evaluated (nutritional assessment, physical examination, and laboratory tests) in this cross-sectional study. Univariate analysis was performed using Mann-Whitney test or Fisher's exact test followed by logistic regression analysis. Presence of dyslipidemia (fasting cholesterol >200mg/dl or triglycerides >130mg/dl) was the dependent variable. 90 children were enrolled. The mean age was 10.6 years (3-16 years), and 52 (58%) were female. LSHIV was detected in 46 children (51%). Factors independently associated with dyslipidemia were: low intake of vegetables/fruits (OR=3.47, 95%CI=1.04-11.55), current use of lopinavir/ritonavir (OR=2.91, 95%CI=1.11-7.67). In conclusion, LSHIV was frequently observed; inadequate dietary intake of sugars and fats, as well as current use of lopinavir/ritonavir was associated with dyslipidemia.