The purpose of this study was to evaluate the caries experience among 6-12-year-old indigenous (Naporunas) and non-indigenous (recent settlers of mixed ethnic origin) schoolchildren, living in the Amazon basin of Ecuador. Cross-sectional data were obtained from 1,449 clinical exams according to the World Health Organization criteria. Nine (7.6%) indigenous and 3 (4.5%) non-indigenous children had no caries experience in their primary dentition at the age of 6. The mean dmft value (SD) among indigenous and non-indigenous children aged 6 was 6.40 (3.36) and 8.36 (3.93), respectively. Sixty-four (54.2%) indigenous and 29 (43.3%) non-indigenous children had no caries experience in their permanent first molars at the age of 6. Only 7 (6.26%) indigenous and 2 (2.60%) non-indigenous children were caries-free at the age of 12. The mean DMFT values (SD) for 12-year-olds were 4.47 (2.85) among indigenous and 5.25 (2.89) among non-indigenous children. Fillings were almost non existent. Caries rates were high among both groups, with untreated carious lesions predominating in all ages. The data of indigenous children suggest adoption of a non-traditional diet. An appropriate oral health response based primarily on prevention and health promotion is needed.