Our study found a U-shaped association between cystatin C levels and obesity in boys, with a decreasing risk of obesity before cystatin C values reached 0.97 mg/L and then increasing; however, in girls, the risk of obesity increased before the cystatin C value reached 0.91 mg/L and then tended to decrease. This evidence concerns the gene CST3 and obesity due to melanocortin 4 receptor deficiency.