This study aimed to determine the effect of metabolic syndrome (MS) on the reproductive function in fertile (FM) and male partners of infertile couples (MPIC). We performed a cross-sectional study formatting two study groups: partners of pregnant women (n = 238; mean age 32.0) as FM and male partners of infertile couples (n = 2642; mean age 32.6) as MPIC. A standard semen analysis was performed and clinical, laboratory and lifestyle data were analysed. The adapted NCEP-ATPIII criteria were used to define MS. 12.2% of FM and 17.8% of MPIC had MS. In both groups, men with MS were older, they were centrally obese and had higher triglycerides, systolic and diastolic blood pressure and decreased HDL cholesterol values as compared to men without MS. However, glucose concentrations as well as fasting insulin levels were significantly higher only in the MPIC-MS+ group. MS was not associated with semen parameters. Testosterone levels were negatively correlated to MS in both groups. This negative association persisted within the BMI categories between MPIC-MS- and MPIC-MS+ groups. LH was negatively correlated to MS but only in MPIC. FSH and oestradiol were not correlated to MS. Smoking and alcohol consumption were higher among men with MS. This study shows that except for testosterone, MS has no independent effect on major fertility parameters in different subgroups of men.