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Background/AimsThe development of nonalcoholic fatty liver disease (NAFLD) is associated with multiple genetic and environmental factors.Methods : We performed a genome-wide association study to identify the genetic factors related to NAFLD in a Korean population-based sample of 1,593 subjects with NAFLD and 2,816 controls. We replicated the data in another sample that included 744 NAFLD patients and 1,137 controls. We investigated single-nucleotide polymorphisms (SNPs) that were related to NAFLD.Results : After adjusting for age, sex and body mass index, rs738409, rs12483959 and rs2281135, located in the PNPLA3 gene, were validated in our population (p<8.56×10−8) in the same linkage disequilibrium block. Additionally, rs2143571, rs3761472, and rs2073080 in the SAMM50 gene showed significant associations with NAFLD (p<8.56×10−8). Furthermore, these six SNPs showed significant associations with the severity of fatty liver (all p<2.0×10−10 in the discovery set and p<2.0×10−6 in the validation set) and NAFLD, with elevated levels of alanine aminotransferase (all p<2.0×10−10 in the discovery set and p<2.0×10−6 in the validation set).Conclusion : sWe demonstrated that the PNPLA3 and SAMM50 genes are significantly associated with the presence and severity of NAFLD in a Korean population. These findings confirm the important roles of genetic factors in the pathogenesis of NAFLD.