Seventy-one asymptomatic human immunodeficiency virus-1 (HIV-1) -infected individuals who underwent colonoscopy for detection of diseases other than amebiasis were included in this study. Ulcerative lesions caused by Entamoeba histolytica were identified by colonoscopy and biopsy in 11.3% (8 of 71) of individuals. Stool microscopic examination hardly identified Entamoeba, whereas serum antibody against E. histolytica was often elevated in patients with subclinical intestinal amebiasis. Human leukocyte antigen (HLA) class II allele against E. histolytica infection (DQB1*06:01) was frequently identified in these patients. This study emphasizes the endemic nature of E. histolytica infection in our cohort and the difficulties in epidemiological control.