Purpose. Evaluate the nutritional status of indigenous and nonindigenous children under 5 in two provinces in the Peruvian Amazon. Methods. Descriptive cross-sectional representative study of families with children under 5 in the provinces of Bagua and Condorcanqui in Peru. The study consisted of an interview with the child's or children's mother or caregiver, anthropometric assessment, capillary hemoglobin measurement, screening for intestinal parasites in children under 5, access to health services, history of acute respiratory infections and acute diarrheal diseases, socioeconomic status, and intake of inadequately iodized salt. Using generalized linear methods, the determinants of chronic malnutrition and anemia in children were identified in each study population. Results. A total of 986 families and 1 372 children were assessed. The prevalence of chronic malnutrition was higher in the indigenous population than in the nonindigenous population (56.2% versus 21.9%); likewise for anemia (51.3% versus 40.9%). The determinants of chronic malnutrition in the two populations differed. In the indigenous population, the main determinants were an age of more than 36 months (OR 2.21; CI95% 1.61-3.04) and substandard housing (OR 2.9; CI95% 1.19-7.11), while in the non-indigenous population, they were extreme poverty (OR 2.31; IC95% 1.50-3.55) and institutional birth (OR 3.1; IC95% 2.00-4.83). Conclusions. There are marked gaps between the indigenous population and the nonindigenous population in terms of living conditions, access to health services, and the nutritional status of children under 5. Particular attention should be paid to the indigenous population to improve the way state programs and services are delivered in these contexts.