Introduction: Indigenous groups face discrimination and exclusion, which generates inequities in the field of health. In addition, they are nutritionally vulnerable, which affects their growth and development potential compared to the non-indigenous population. Objective: to compare the nutritional status and anthropometric measurements between Zapotec and non-Zapotec schoolchildren from a region of Oaxaca, Mexico. Material and methods: cross-sectional descriptive study in a representative sample of 477 schoolchildren aged 8 to 11 years from a municipality in Oaxaca. The population was divided into Zapotec (Zap+) and non-Zapotec (Zap-). Weight, height, waist circumference, arm circumference and triceps fold were obtained. BMI was calculated for age, waist-to-height ratio, and indicators of the fat and muscle component of the arm. The chi square and Fisher's exact tests were used for proportional differences. Results: 51.5% of schoolchildren were Zap+ and a high prevalence of overweight and obesity of 33.7% was reported. Zap+ girls had a higher prevalence of wasting (p=0.032) and Zap+ boys had a lower % arm fat area (0.004). Among Zap- boys and girls, boys had low weight (p=0.040) and reduced musculature (p=0.003), while girls had a higher proportion of fat above average (p=<0.001). Zap- children had a higher prevalence of stunting compared to Zap+ children (p=0.022). This difference was maintained until age 11 (p=0.007). It was observed that 11-year-old Zap+ girls had less muscle (p=0.001) and a higher cardiovascular risk (p=0.032) compared to Zap- girls. Conclusions: Positive secular changes were observed in Zap+ boys, reflected in greater height than Zap+ girls and Zap- boys, and a trend in increasing BMI and cardiovascular risk in Zap+ girls, which could reflect a possible nutritional transition.