Children in the Bolivian Andes are exposed to endemic infections and meager nourishment, and live under poor hygienic conditions. The prevention of children malnutrition is a priority in many countries including Bolivia. In this study, the health status of schoolchildren in Taraco, a Puna district, at 4,000 meters above sea level (masl) and in Caranavi, at 650 masl in the wealthier subtropical valleys, was compared. The weight, height, and hematological and biochemical parameters in blood, parasites in stool, and clinical information in 120 children from rural Taraco and in 96 from semi-urban Caranavi, both predominantly of Aymara ethnicity, were registered. Eleven percent of Taraco children were undernourished compared with 3% in Caranavi. Instead, 41% of the children in Caranavi were obese or overweight, compared with 8% in Taraco. Anemia was found in 74% of the children in Taraco compared with 7% in Caranavi. Albumin levels were normal in all samples, albeit lower in Taraco. Similar and normal serum zinc levels were measured in both groups. Approximately 60% of the children in both locations showed insufficient vitamin D levels, with lower levels in Taraco children. Hymenolepis nana and Entamoeba coli, parasites determinant of poor hygienic conditions, were respectively detected in 78% and 21% of fecal samples from Taraco, and in 29% and 8% of samples from Caranavi. We show increased anemia, nutritional deficiencies, and indications of poor hygienic conditions in highlands compared with lowlands. The prevalence of obesity in the lowlands demands addressing diverse nutritional deficiencies in the regions of Bolivia.