This study aimed to determine the prevalence of Entamoeba histolytica in BASECO, an urban slum community situated in Manila Harbor, Manila, Philippines using stool enzyme-linked immunosorbent assay (ELISA). It also aimed to determine if age, sex, and geographic location are contributory factors to the prevalence of E. histolytica. Stool samples were collected from 627 urban slum community residents of BASECO. Samples were viewed under light microscopy and the different parasites observed were identified. Stool ELISA was done using E. histolytica II antigen detection kits (TECHLAB®). Using E. histolytica II kits, E. histolytica had a prevalence of 9.09% (5/55) among the microscopically-positive samples for E. histolytica/E. dispar indicating a greater prevalence for the nonpathogenic species. No significant difference was observed in the prevalence of infection across all three variables: age, sex and geographic location. The overall prevalence of E. histolytica in BASECO, Manila, Philippines is 0.797% (5/627) which is lower than previous studies done on estimating the prevalence of E. histolytica using various techniques.