In Japan, amebiasis has been observed in homosexual men, in institutionalized persons, and in overseas travelers. We have previously reported an outbreak of amebiasis that occurred from 1986 to 1994 in institutions for the mentally retarded in Kanagawa and Shizuoka Prefectures in Eastern Japan. Entamoeba histolytica but not Entamoeba dispar was identified in Entamoeba cultures obtained from cyst passers in four institutions located in different municipalities in this region. In the present study, serine-rich protein genes of eight isolates from the four institutions were sequenced, and their polymorphism was analyzed. The results showed that all the sequences from the E. histolytica isolates were identical. This retrospective study led us to conclude that the outbreak of amebiasis in different municipalities was derived from a single source of E. histolytica.