We determined yearly change in prevalence and risk factors for amebic colitis caused by intestinal invasive amebiasis among persons who underwent endoscopy and assessed differences between HIV-positive and HIV-negative persons in Japan. A total of 10,930 patients were selected for analysis, of whom 54 had amebic colitis. Prevalence was in 2009 (0.88%, 12/1360) compared with 2003 (0.16%, 3/1904). Male sex (odds ratio [OR] 8.39, 95% CI 1.99-35.40), age <50 years (OR 4.73, 95% CI 2.43-9.20), history of syphilis (OR 2.90, 95% CI 1.40-5.99), and HIV infection (OR 15.85, 95% CI 7.93-31.70) were independent risk factors. No differences in risk factors were identified between HIV-positive and HIV-negative patients. Contact with commercial sex workers was a new risk factor among HIV-negative patients. Homosexual intercourse, rather than immunosuppressed status, appears to be a risk factor among HIV-positive patients.