Mercury is a hazardous metal responsible for environmental contamination and human intoxication. Methylmercury, a very toxic organic compound, bio-accumulates through food chain, and is responsible for chronic mercury exposure of riverside Amazonian communities with a diet rich in fish. Uncertainties about the reference exposure dose that could have damaging consequences for nervous system development makes necessary the biomonitoring of these Amazonian populations, especially children. In this work, a comparative study was performed in exposed and non-exposed children living in the Amazon. A total of 168 children were analyzed to find possible correlations between gender, age, location, and hair mercury content. For each location, no statistically significant differences (P<0.05) were detected for gender and age versus mercury content. However, mean mercury levels in hair samples may indicate a tendency of boys to average higher hair concentrations. Also, in the community with highest levels of mercury, the limit of 10 micro g/g of mercury was surpassed by 65% of 2-6 years and 50% of 7-12 years children but only by 27% of 0-1 year babies, pointing to a lower bioaccumulation and/or the existence of a protection mechanism in babies. Log normal distributions of mercury concentrations for each location showed that children from populations under influence of gold mining activity contain the highest mercury levels in hair samples, though this intoxication may have decreased when compared to previous studies. Knowledge originated by this monitoring will better assist in the development of prevention strategies and government actions targeting the mercury contamination of Amazonian environment.