Our investigation aimed at evaluating the relationship between metabolic syndrome, alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma glutamyl transferase (GGT), and alkaline phosphatase (ALP) in the Rafsanjan cohort study (RCS). We used data obtained from the RCS, as a part of the prospective epidemiological research studies in Iran. In this cross-sectional research, 9895 participants from the baseline phase of RCS who completed medical questionnaire were included. Metabolic syndrome (MetS) defined using NCEP-ATP III criteria. The relationship between elevated serum liver enzymes levels even within the normal range and metabolic syndrome was evaluated by logistic regressions. The prevalence of MetS was 34.42% in the participants of study. The mean concentrations of AST, ALT, ALP, and GGT increased with increasing MetS components. After adjusting for all potential confounders, elevated serum concentrations of ALT, AST, GGT, and ALP even within the normal range were related with an increased odds of MetS. MetS was associated with increased levels of liver enzymes even within the normal range. These results indicated the potential for elevated liver enzymes as biomarkers for the possible presence of MetS.