A cross-sectional study was performed in February 2001 to evaluate the prevalence and risk factors of Blastocystis hominis infection in army personnel who resided in an army base in Chonburi, Thailand. A total of 904 army personnel were enrolled in this study. Short-term in vitro cultivation was used to detect B. hominis in stool samples. In this population, B. hominis was the parasite most frequently found, and was identified in 334 of 904 stool specimens (36.9%). A significant association between B. hominis infection and symptoms was identified that might emphasize the role of B. hominis as a human pathogen. After adjustment for potential confounders, significantly increased risk of being infection with B. hominis was associated with being a private, working in a specific unit, and consuming unboiled drinking water. Thus, waterborne transmission of B. hominis infection was indicated at this army base. However, other modes of transmission cannot be ruled out.