The aim of the present study was to examine the causal-effect of baseline (year 2004) serum γ-glutamyl transpeptidase (GGT) level with the prevalence of metabolic syndrome (MS) in year 2008. The study was comprised of male workers who underwent a regular health check-up in 2004 and 2008. MS was diagnosed according to the American Association of Clinical Endocrinologists (AACE) criteria. In the subgroup analysis according to serum GGT level, triglyceride (TG), low density lipoprotein cholesterol (LDL-C), and total cholesterol (TC) showed a significant increasing tendency (p < 0.001). In addition, unexpectedly results were consistent in non-drinkers (p < 0.001). GGT level was significantly associated with risk factors of MS (waist circumference [WC]: r = 0.18, p < 0.001; fasting blood glucose [FBG]: r = 0.16, p < 0.001; TG: r = 0.29, p < 0.001). As the secondary biomarker, homeostasis model assessment of insulin sensitivity (HOMA-S) and TC had significant correlations with GGT level (HOMA-S: r = -0.14, p < 0.001; TC: r = 0.21, p < 0.001). In the 4-year prospective analysis, the predictive effect of baseline GGT concentrations on change in MS status was evaluated using Cox proportional model. Elevated GGT concentrations measured in 2004 were associated with the risk of MS incidence after 4 years (GGT: HR 1.7 [95% CI: 1.2-2.3]) (p < 0.01). This observation indicates that an elevated GGT level could be suggested as a subsidiary marker for MS and partially reflects dyslipidemia as a component of MS.