Background: Non-alcoholic fatty liver disease (NAFLD) is an important cause of chronic liver diseases around the world. Paraoxonase-1 (PON1) is an enzyme produced by the liver with an important antioxidant role. The aim of this study was to evaluate PON1 serum concentration and PON1 gene polymorphisms in patients with NAFLD. Materials and methods: We studied a group of 81 patients with NAFLD with persistently elevated aminotransferases and a control group of 81 patients without liver diseases. We collected clinical information and performed routine blood tests. We also measured the serum concentration of PON1 and evaluated the PON1 gene polymorphisms L55M, Q192R, and C-108T. Results: There was a significant difference (p < 0.001) in serum PON1 concentrations among the two groups. The heterozygous and the mutated homozygous variants (LM + MM) of the L55M polymorphism were more frequent in the NAFLD group (p < 0.001). These genotypes were found in a multivariate binary logistic regression to be independently linked to NAFLD (Odds ratio = 3.4; p = 0.04). In a multivariate linear regression model, the presence of NAFLD was associated with low PON1 concentration (p < 0.001). Conclusions: PON1 serum concentrations were diminished in patients with NAFLD, and the presence of NAFLD was linked with low PON1 concentration. The LM + MM genotypes of the PON1 L55M polymorphism were an independent predictor for NAFLD with persistently elevated aminotransferases. Author Contributions: Conceptualization, M.V.M., L.C., I.C.B. and M.A.; methodology, M.V.M., L.C., M.A., and S , .C.V.; validation, M.A., L.C., D.M.M., V.N., D.S. and S.P.; formal analysis, S , .C.V.; investigation, M.V.M., L.C., R.M.P., I.C.B. and S.P.; resources, I.C.B., S , .C.V., R.M.P., D.M.M., A.D.B. and A.L.R.; writing-original draft preparation, M.V.M.; writing-review and editing, S , .C.V., L.C., I.C.B. and M.A.; visualization, A.L.R.; supervision,