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To determine if genetic diversity of Blastocystis hominis exists in Japan, we monitored 64 B. hominis-infected people: 39 asymptomatic people whose infections were detected during routine medical check-ups (32 Japanese and 7 non-Japanese) and 25 patients with gastrointestinal symptoms who visited the outpatient clinics of St. Luke's International Hospital (19 Japanese and 6 non-Japanese). We detected 6 known and 2 new riboprint patterns in isolates from the infected people. There were no differences in the distribution of ribodemes between isolates from Japanese and non-Japanese people, similar to that in other countries. However, we noted a possible relationship between ribodeme type and pathogenicity. The results suggest that ribodemes I, III, and VI may be responsible for gastrointestinal symptoms.