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In February 2005, we conducted a cross-sectional study to determine the prevalence and the risk factors of giardiasis in 531 primary schoolchildren of a rural community, Chacheongsao province, Thailand. Using both sedimentation and flotation techniques to detect Giardia duodenalis, the prevalence of giardiasis was 6.2%. Assemblage A, subgenotype II and assemblage B, subgenotype IV were identified by PCR-RFLP of glutamate dehydrogenase gene. Our data might indicate that, in this population, only assemblage A, subgenotype II of G. duodenalis was transmitted via water. Using multivariate analysis, significant risk factors for giardiasis were children of age 5–9 years, households with ≥ 3 children under the age of 12 years, low parental educational level, drinking bottled water, and living in close contact with dogs. Washing hands before meals had a protective effect. From these significant risk factors, multiple modes of transmission of G. duodenalis were suggested in this population.