Non-alcoholic fatty liver disease (NAFLD) in children has been recognized as a major health burden. The high prevalence of NAFLD is probably due to the contemporary epidemics of obesity, unhealthy dietary pattern, and sedentary lifestyle. The purpose of this study was to investigate anthropometric, biochemical and dietary intake parameters of obese Greek children with and without NAFLD. Eighty two obese children aged 8–15 (45 boys/37 girls) participated in the study. Ultrasonography (US) was used to diagnose NAFLD in all participated subjects. Liver indexes were measured in all children. A 3-day dietary was recorded for all subjects. Data for continuous variables is expressed as mean values±standard deviation. Thirty-five out of eighty two subjects (42.6%) had NAFLD. Body Mass Index levels (P<0.001) and Waist Circumference (P<0.046) levels were statistically higher in the children with severe NAFLD (37.2kg/m²±6.2 and 102.9cm±14) compared to children with mild NAFLD (26.6kg/m²±3.3 and 86.1cm±9.9) and absent of fatty liver (25.3kg/m²±3.6 and 85.2cm±11.2), respectively. Total carbohydrates intakes were significantly higher in subjects with NAFLD (288.8g±70.6) compared to children without NAFLD (244.5g±67.5), (P<0.001). Saturated fatty acids (SFAs) intake was proportionally increased to the degree of hepatic steatosis, while n-3 fatty acids (n-3 FA) consumption was inversely related with NAFLD. In multiple regression analysis of factors associated with NAFLD, HOMA-IR (OR: 1.260, 95%CI: 1.110–1.470, P<0.001) and n-3FA (OR:1.921, 95%CI:1.132–2.187, P<0.001) were the most significant ones. Our results showed that IR, high dietary intakes of CHO and SFA and a low dietary consumption of fiber and n-3 FA were positively associated with the pathogenesis of NAFLD.