Apelin is a new adipokine associated with obesity. Data about the relationship of apelin to the metabolic syndrome (MS) are still scarce. Late-onset hypogonadism (LOH) is common in men with MS, but we did not find data about the levels of apelin in men with LOH. The aim of this study is to determine the levels of apelin in men with MS with or without LOH. Patients and Methods: 99 men are included in the study. Of them 65 have MS (IDF 2005) and they are divided according to their morning total testosterone (TT) level (cutoff 10.4 nmol/l) into two groups: MS-low T (N = 21) and MS-normal T (N = 44). The control group consists of 34 men without MS and with normal T. Apelin is determined in serum using enzyme linked immunosorbent assay. Some of the men were additionally assigned to testosterone treatment and monitored. Results: MS men are at mean age (±SD) = 50.4 ± 9.6 years and TT = 13.6 ± 5.4 nmol/l. The control group is at age = 51.5 ± 6.4 years (NS) and TT = 17.9 ± 5.6 nmol/l (p < 0.001). The levels of apelin are higher in the MS group—1.61 ± 0.53 ng/ml compared to the control one—1.38 ± 0.57 ng/ml (p < 0.05). There is no difference between MS-lowT—1.53 ± 0.52 ng/ml and MS-normal T —1.65 ± 0.53 ng/ml sub-groups. The MS-normal T differs from the control group (p < 0.05). Significant correlation of testosterone with apelin levels is not found. Although apelin correlates with other laboratory parameters: LDL-levels in the MS-patients (Pearson’s = 0.311, p < 0.05); HbA1c in men with T2DM (Pearson’s = 0.285, p < 0.05); serum creatinine levels (Pearson’s = 0.257, p < 0.001). The patients that are assigned to testosterone substitution show a trend for lowering apelin levels. Conclusions: In this study, higher apelin levels are found in the presence of MS compared to healthy men, but do not differ between men having MS with low or normal T.