An epidemiological study was conducted on a population attending outpatient clinics in Manaus, Amazon, Brazil to determine the prevalences of infection by the Entamoeba histolytica/E. dispar complex and by E. histolytica alone, as well as to identify the risk factors involved in transmission. The study was conducted in two phases: survey and case-control. Face-to-face interviews were carried out and faecal samples collected from 1578 individuals. Faeces were examined by optical microscopy and tested for the pathogenic E. histolytica specific antigen. Positivity to E. histolytica/E. dispar was 21.5% (340 cases). Cases were compared with 340 control samples, negative for the E. histolytica/E. dispar complex based on examination by optical microscopy. The analysis was conducted by logistic regression. The risk factors identified were: place of residence, age, ingestion of raw vegetables, quality of water consumed, number of rooms and bedrooms per house, and having other protozoan infections. Specific antigen detection tests identified 22 participants infected by E. histolytica (6.8%) among those positive for E. histolytica/E. dispar. There was a higher proportion of males among participants infected by E. histolytica than among those with E. dispar infections. The study population was asymptomatic or presented non-specific symptoms that could be attributed to amoebiasis.