An increase in the prevalence of non-alcoholic fatty liver disease (NAFLD) is related to an elevation in obesity worldwide. NAFLD is a prevalent liver disorder characterized by excessive lipid accumulation in hepatocytes, primarily induced by a high-fat diet (HFD). NAFLD not only affects the liver but also has significant implications for other organs, including the kidney and heart. The Hedgehog pathway, a critical signaling cascade involved in cellular processes and development, has emerged as a potential player in the pathogenesis of NAFLD and its extrahepatic effects. The purpose of the present study was to study impacts of choline and vitamin E co-treatment on the molecular and histopathological changes in heart and kidney in an obese rat model with NAFLD induced by a high-fat diet. Fifty albino rats were grouped into five equal groups randomly. The first one was kept as a control group the remaining four groups were treated as follows; G2: NAFLD, G3: NAFLD and received low dose of choline (25 mg/kg BW orally) and vitamin E (50 mg/kg BW orally), G4: NAFLD and received medium dose of choline (50 mg/kg BW orally) and vitamin E (100 mg/kg BW orally) and G5: NAFLD and received high dose of choline (100 mg/kg BW orally) and vitamin E (200 mg/kg BW orally). The results revealed that treating rats with varying dosages of choline and vitamin E significantly reduced Hhip, Ptch1, Smo and Gli1 hepatic mRNA expression in choline and vitamin E co-treated groups in comparison to NAFLD group and histologically displayed ameliorative consequences on kidney and heart tissues. In conclusion, choline and vitamin E co-treatment relieves the molecular and histological consequences of NAFLD in rats, with dose dependent manner.