To determine the prevalence of dyslipoproteinemia on a large juvenile systemic lupus erythematosus (jSLE) cohort, we selected 40 patients after rigorous exclusion criteria. Lipoprotein levels were determinated after 12 hours fast and risk levels for CAD were defined by standards of the Brazilian Guidelines for dyslipoproteinemia according to US-NCEP. All individuals were under steroid therapy and chloroquine and 43% had active disease. Thirty patients (75%) had high-risk levels for CAD (23 isolated low HDL, while in seven subjects low HDL was associated to high TG in four, high LDL in one, high TG/LDL in one and high TC/LDL in one). Remarkably, overall analysis revealed that 85% patients were included in high/medium risk levels group (29% for TC, 29% for LDL, 88% for HDL, and 18% for TG) and these disturbances occured mainly in the first four years of disease. Unexpectedly, one-third of the patients presented two or more high/medium lipoprotein risk factors. Independently, active jSLE was associated to TG (OR = 3.2; P < 0.001) and had a tendency towards reduction on HDL (OR = 8.5; P = 0.056). Considering improvements on jSLE outcome, the increased frequency of high/medium lipoprotein risk levels for CAD reinforces the need of prevention measures in order to minimize deleterious effects of this disturbance.