ObjectivesTo study the somatotype variations adjusted by altitude, age, sex, and BMI categories, and to assess the health status of the children population.MethodsA sample of 460 children aged 8–13 years was assessed in a cross‐sectional study conducted on anthropometric measurements between 2011 and 2015. Data were categorized into two age groups: Group 8–10, Group 11–13 and two altitudes: Highland (>2000 masl), lowland (<2000 masl). The somatotypic profile was determined by the Heath and Carter's study method and the Body Mass Index was used to assess children nutritional status. Generalized linear latent variable models (GLLVM) were performed to test the association between somatotype and geographic altitude. Individual age‐sex specific somatotypes were plotted in a two‐dimension somatochart, and group dispersion was displayed by the somatotype attitudinal mean.ResultsThe sample has an overall endomorph‐mesomorph body type, exhibiting different patterns when altitude and sex were considered. The GLLVM showed that the whole somatotype was different by altitude. Highland children occupied central to endomorphic‐mesomorphic places in the somatochart with lower variation. In both altitudes, girls exhibited higher endomorphy than boys. Several discrepancies between the BMI categorization and the somatotype were observed.ConclusionsJujenean children show differential body patterns across geographic altitude which exhibit age and sex variations. Children have a differential tendency to a fat mass gain. The BMI showed some inconsistencies with somatotype, leading to a misclassification of the child nutritional status, this highlights the importance of not to treat the BMI in isolation but with other determinants of the health status.