Objectives Market integration is an important source of cultural change exposing indigenous populations to epidemiologic and nutrition transitions. As children and adolescents are biologically sensitive to the health effects of market integration, we examine community variation of anthropometric indicators of nutritional status and growth among a cross‐cultural sample of Kichwa, Shuar, Huaorani, and Cofán indigenous groups in the northern Ecuadorian Amazon. Methods We measured height, weight, body mass index (BMI), upper arm circumference, and triceps skinfolds of 186 children and adolescents aged 2 to 18 years from seven communities. Anthropometric z‐scores were calculated based on the National Health and Nutritional Examination Survey. Comparisons were made with this US reference group, along with between community differences to contextually explore the impacts of varying degrees of market integration. Results We found a high prevalence of stunting in both boys (40%) and girls (34%). Adiposity increased with age and 40% of girls between 15 and 18 years old were overweight. There were large sex differences in body composition with higher BMI, arm circumference, and triceps skinfolds in adolescent girls. The Kichwa demonstrated the poorest growth outcomes and nutritional stress followed by the Huaorani and Shuar; yet distinctions in under‐ and over‐nutrition were evident within groups. Conclusion Market integration is a major factor influencing the developmental and lifestyle mismatch associated with the epidemiologic and nutrition transition in general, and the dual burden pattern of high rates of stunting yet adequate to above average short‐term nutritional status indicators found among indigenous Amazonian populations. Am. J. Hum. Biol. 25:524–533, 2013. © 2013 Wiley Periodicals, Inc.