Abstract Objectives Little is known about hepatitis A virus (HAV) prevalence in indigenous communities. This study aims to evaluate the prevalence of HAV in indigenous community compared to urban population located at Western Amazon in Brazil. Results A total of 872 serum samples were obtained from 491 indigenous and 381 non indigenous individuals aging 0 to 90 years. Samples were tested for total and IgM anti-HAV and positive IgM samples were tested for HAV RNA. The overall prevalence of total anti-HAV was 87%, increased according age showing 100% of prevalence in those aging more than 30 years (p < 0.0001) and it was similar among indigenous and urban population. Total anti-HAV prevalence varied between tribes (p < 0.0001) and urban sites (p = 0.0014) and spatial distribution showed high prevalence in homes that received up to 100 dollars. IgM anti-HAV prevalence was 1.7% with predominance in males, those aging more than 41 years. No HAV RNA was detected. In conclusion, high overall anti-HAV prevalence was found in indigenous communities in North Brazil demonstrating the importance of universal vaccination in this group.