Background and Aim. Overweight prevalence in children and adolescents shows great variability which is related to individual-level and environmental-level factors. The present study aimed to determine the prevalence of and factors associated with overweight in Peruvian children and adolescents living at different altitudes. Methods. 8568 subjects, aged 6-16 y, from the sea level, Amazon, and high-altitude regions were sampled. Overweight was identified using BMI; biological maturation and physical fitness were measured; school characteristics were assessed via an objective audit. Results. Overweight prevalence decreased with age (28.3% at 6 y to 13.9% at 16 y); it was higher in girls (21.7%) than boys (19.8%) and was higher at the sea level (41.3%), compared with Amazon (18.8%) and high-altitude (6.3%) regions. Approximately 79% of the variance in overweight was explained by child-level characteristics. In Model 1, all child-level predictors were significant (p<0.001); in Model 2, six out of nine added school-level predictors (number of students, existence of policies and practices for physical activity, multisports-roofed, duration of Physical Education classes, and extracurricular activities) were significant (p<0.001); in Model 3, subjects living at high altitudes were less likely to be overweight than those living at the sea level. Conclusions. Child- and school-level variables played important roles in explaining overweight variation. This information should be taken into account when designing more efficient strategies to combat the overweight and obesity epidemic.