We report an exceptionally high rate of infection by Haplorchis taichui (Nishigori, 1924) in human populations on Mindanao Island, southern Philippines. This intestinal fluke is seldom encountered, and this is the first report of high prevalence of infection (36%) in humans by H. taichui in the Philippines. The likely source of haplorchine infection has been linked to consumption of raw or undercooked freshwater fish containing infective metacercariae. The most common clinical symptoms appeared as upper abdominal discomfort or pain and borborygmi. Praziquantel (75 mg/kg divided in 3 doses in 1 day) was a well-tolerated and effective treatment for infection by H. taichui.