BackgroundTo describe the biomarkers of lipid metabolism in children and adolescents with polyarticular and systemic JIA and to relate them to diseases subtypes, diseases activity markers, and nutritional status.MethodsA cross-sectional study including 62 JIA patients was performed. The following variables were evaluated: disease activity and medications used, body mass index, height for age (z-score), skin folds (bicipital, tricipital, subscapular and suprailiac), food intake based on three 24-h food recalls, lipid profile (total cholesterol (CT), low-density lipoprotein (LDL), high-density lipoprotein (HDL), triglycerides (TG) and non-HDL (N-HDLc), glycemia and insulin, erythrocyte sedimentation rate (ESR), ultrasensitive C-reactive protein (us-CRP) and apolipoproteins A-I and B (Apo A-I and Apo B).ResultsDyslipidemia was observed in 83.3% of the patients. Based on classical lipid profile, low HDL-c levels was the most frequently alteration observed. Inadequate levels of LDL-c, Apo B and NHDL-c were significantly more frequent in the systemic JIA subtype when compared to the polyarticular subtype (p = 0.017, 0.001 and 0.042 respectively). Patients on biological therapy had a better adequacy of Apo A-I concentrations. The ESR showed a negative correlation with Apo A-I level (r = − 0.25, p = 0.047).ConclusionWe concluded that dyslipidemia is common in patients with JIA, especially in systemic subtype. The systemic subtype and an elevated ESR were associated with lower concentrations of Apo A-I, suggesting the participation of the inflammatory process.