Background: High blood lead levels (BLLs) have been previously reported in indigenous people living in communities in the northern Peruvian Amazon. Oil extraction activities have been conducted in the area since the 1970s and have been identified as a source of lead exposure. Objective: Measure BLL and assess risk factors associated with BLL among indigenous populations from four river basins of the northern Peruvian Amazon. Methods: Participants from 39 communities were selected using a two-stage stratified random selection strategy and were visited between May and June 2016. Information on risk factors was collected using structured questionnaires and blood samples were taken. Overall, complete information was available from 1047 individuals (309 < 12 years old, 738 ≥ 12 years). BLL was determined using atomic absorption spectrophotometry in a graphite chamber. Weighted linear logistic regression models were used to study the association between socio-demographic variables, self-reported life-style factors, environmental, geographical and occupational exposures and BLLs. Results: Geometric mean (95% CI) BLL was 4.9 (4.5, 5.4) µg/dL in participants <12 years and 5.7 (5.4, 6.0) µg/dL in older participants. There were marked differences in BLL between river basins with the highest levels observed in the Corrientes river basin [8.1 (7.2, 9.1) µg/dL <12 years and 8.8 (8.0, 9.6) µg/dL older participants]. High BLL was associated with older age, being male, living in the Pastaza, Tigre or Corrientes river basins and consumption of fish offal in children and adults. Increased Euclidean distance between residence and oil production facilities was associated with a small reduction in BLL. Conclusion: BLLs that pose a health risk were detected in the study population of a non-industrialized and remote area of the Amazon. The highest BLLs were observed in those river basins where relative oil extraction activity and environmental levels of contaminants have been reported to be greatest.