Amoebiasis is an infection caused by water borne protozoan parasite Entamoeba histolytica. In Uganda where sanitation infrastructure and health education are not adequate, amoebiasis is still be an important health problem. However, there was little or no data on prevalence of this parasite in Uganda. This information was needed for decision making in order to allocate limited public health resources for treatment and prevention of amoebiasis. Currently there is a feasibility of development of amebiasis vaccine, therefore such studies could strengthen the urgency of this innovation. Routine microscopy procedures were used for detection of Entamoeba histolytica among patients presenting with clinical signs associated with amoebiasis in selected health facilities in Soroti, Eastern Uganda. Direct examination of wet stool was done. Of the 301 stool samples examined, 60 (19.93%) were found to be positive for Entamoeba histolytica/dispar. Infection with Entamoeba histolytica/dispar was significantly higher (P<0.05) among males (22.14%) compared to 17.39% among females. The prevalence was significantly higher (P<0.05) in 6-12 years age group (22.4%) than in 13-19 years age group (17.65%). In conclusion amoebiasis was an important health problem in Soroti and probably Uganda as a whole. However since Entamoeba histolytica and E.dispar are morphologically similar, it is recommended that molecular studies characterize them so that true prevalence of pathogenic Entamoeba histolytica can be determined.