OBJECTIVE: To provide some of the first data on cancer incidence among indigenous people in the Amazon basin of Ecuador, and to compare that incidence with the level found among nonindigenous persons living in that same area. METHODS: From the study area 1 207 cancer cases were reported to the National Cancer Registry over the 1985-2000 period. Frequency and relative risks were calculated for the indigenous residents and for the nonindigenous residents of the area. RESULTS: Cancer of the testes and leukemia were the most common cancer types among indigenous men, and cancer of the cervix uteri was the most common among indigenous women. Indigenous men were at significantly lower risk for cancer of the stomach, skin, prostate, and lymph nodes and for leukemia than were nonindigenous men. Indigenous women were at significantly lower risk for cancer of the stomach, skin, breast, cervix uteri, and lymph nodes than were nonindigenous women. CONCLUSION: Our data from the Ecuadorian Amazon indicate the need to develop appropriate mechanisms to register the indigenous population in the national census as well as in the National Cancer Registry. Also needed are cancer early detection programs, more health education efforts, and stronger health services that are adapted to the local conditions. Future research should focus on factors that may help to explain the different cancer patterns found among indigenous persons and nonindigenous persons.