Abstract. A cross-sectional study was performed to determine the prevalence of giardiasis in hilltribe children of 2 different remote districts (Mae-chaem and Hod), Chiang Mai, Northern Thailand from November 2006-April 2007. The overall prevalence of giardiasis was 5.2%. Genetic characterization of Giardia duodenalis isolated from these children was performed using PCR methods specific for small subunit ribosomal rRNA (SSU-rRNA) and glutamate dehydrogenase (gdh) gene. This study shows that the distribution of Giardia assemblages varied in these 2 populations. Assemblage BIV was found predominantly in children from Hod District while assemblage AII was more common in children from Mae-Chaem District. Our result showed that assemblage A was significantly associated with loose/watery stool (p= 0.001). In addition, children harbouring assemblage B had shed a significantly higher number of cysts (p= 0.019) in stools than those infected with assemblage A. Further study on the epidemiology of giardiasis especially risk factors associated with genotyping would help to understand the nature of this disease in each population.