Environmental and genetic factors have a crucial role in the development and progression of non-alcoholic fatty liver disease (NAFLD). The aim of the present study is to investigate the association between single nucleotide polymorphism (SNP) rs738409 in PNPLA3 gene and rs1260326 in GCKR gene and the development of NAFLD in obese Egyptian population. Forty obese subjects (20 with NAFLD and 20 without NAFLD) and 20 control subjects were enrolled in this study. All subjects were genotyped for (rs738409) PNPLA3 and (rs1260326) GCKR gene polymorphisms using the TaqMan assay. Results revealed that the homozygous mutant GG genotype of the PNPLA3 was the most frequent among patients with NAFLD (15%) as compared to controls (0%) (p=0.036). Regarding the GCKR rs1260326; the homozygous mutant TT genotype was most frequent among patients with NAFLD (40%) as compared to controls (20%) with trend significance (p=0.083) and as compared to obese non-FL group (10%) (p=0.014). The frequency of the T allele was found to be significantly higher in NAFLD patients (62.5%) compared to obese non-FL group (42.5%) (p=0.037). In conclusion our study confirmed the association between PNPLA3 (rs738409) and GCKR (rs1260326) polymorphisms and susceptibility to NAFLD.