Introduction and Aims: Non-alcoholic fatty liver disease (NAFLD) is a spectrum of diseases ranging from simple steatosis without inflammation or fibrosis to nonalcoholic steatohepatitis and in the Western countries has become one of the most prevalent chronic liver diseases related to metabolic and lipid alterations. Cholesteryl ester transfer protein (CETP) participates in high density lipoprotein (HDL)-cholesterol metabolism. The aim of our study was to investigate the influence of polymorphism (rs1800777) of CETP gene on liver histological changes, biochemical parameters, and serum adipokines levels in patients with NAFLD. Material and Methods: A population of 90 patients with NAFLD was recruited in a cross-sectional study. A biochemical analysis (glucose, c-reactive protein, insulin, homeostasis model assessment-insulin resistance, total cholesterol, low density lipoprotein (LDL)-cholesterol, HDL-cholesterol, triglycerides blood, and adipokines (leptin, adiponectin, and resistin) was realized. Genotype of polymorphism (rs1800777) of CETP gene was studied. Results: Eighty-three patients (92.2%) had the genotype GG (wild type group) and 7 patients (7.8%) had the genotype GA (n = 7) or AA (n = 0; mutant type group). Patients with A allele show significant decrease in liver biochemistry parameters – Alanine amino transferase (delta 10.1 ± 9.9 UI/L; p = 0.01), aspartate aminotransferase activity (delta 13.3 ± 9.5 UI/L; p = 0.02), and gammaglutamine transferase levels (delta 39 ± 30.1 UI/L; p = 0.01). Logistic regression analysis indicated that subjects with A-allele carriers were associated with a decreased risk of lobulillar inflammation (OR 0.18, 95% CI 0.04–0.95, p = 0.04) and a decreased risk of steatosis (OR 0.13, 95% CI 0.02–0.89, p = 0.04). Conclusions: A variant of the polymorphism rs1800777 of CETP gene is independently associated with the presence of steatosis and lobulillar inflammation in subjects with proven biopsy NAFLD.