Subclinical hypothyroidism (SCH) is a prevalent condition among adult population, however it is frequently overlooked. Thyroid functions affect metabolic syndrome (MetS) parameters including HDL cholesterol, triglycerides, blood pressure and plasma glucose. On the other hand, the relation between MetS and thyroid dysfunction is not clearly identified yet. The aim of the present study was to investigate the prevalence of SCH among MetS patients and to identify its relation with MetS parameters. Two hundred and twenty MetS patients (MetS group; 167 female, 53 male, mean age: 48.5 ± 11.3) and 190 patients without MetS (Control group; 142 female, 48 male, mean age: 46.3 ± 11.9) attending consecutively to Internal Medicine outpatient clinics were included in this study. Groups were compared in terms of SCH prevalence. SCH was defined as a condition with high thyrotrophin and normal free thyroxine levels. SCH was found in 36 (16.4%) cases in the MetS group and in 11 (5.8%) cases in the control group (p = 0.001). Only female gender was associated with the presence of SCH. About one sixth of MetS patients had SCH. This finding indicates a need for investigating the presence of SCH during the management of MetS patients.