BACKGROUND To study the relationship between lipid profile and body mass index (BMI) in children after a 5-year follow-up. METHODS A total of 281 children were evaluated at the ages of 6 and 11 years. Total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and apoproteins A1 (Apo A) and B100 (Apo B) were measured. Low-density lipoprotein cholesterol (LDL-C) was determined and the Apo B/Apo A, TC/HDL-C, LDL-C/HDL-C indexes, and the atherogenic index were calculated. BMI was also calculated (BMI 5 kg/m2). Evolution parameters were calculated (EVO 5 value 11 years - value 6 years). Associations between BMI and lipid profile were studied. RESULTS The prevalence of obesity (according to the criteria of the International Obesity Task Force) was 4.98 % (6 years) and 16,72 % (11 years). In children who were in the fourth BMI quartile at the age of 11 years, LDL-C/HDL-C and TC/HDL-C levels were significantly higher and than those in children in the first quartile but HDL-C and Apo A levels were lower. A significant positive correlation was found between the evolution of BMI and the four indexes studied and TG, but this correlation was negative for HDL-C and Apo A. The evolution of the indexes was positive in 11-year-old obese children and negative in nonobese children. CONCLUSIONS Lipid profile was worse in 11-year-old children in the fourth BMI quartile than in the remaining children. Obese children had higher values of the indexes studied, supporting the importance of obesity as a cardiovascular risk factor.