Patients with polycystic ovary syndrome (PCOS) have an increased prevalence of metabolic syndrome (MBS). Hypoadiponectinemia is closely associated with MBS. The aim of our study was to evaluate the association of adiponectin levels with MBS in patients with PCOS. We studied 60 patients with PCOS and 60 age-matched control subjects. Serum adiponectin, fasting glucose, triglycerides, high-density lipoprotein (HDL) levels, blood pressure and waist circumference were measured for each subject. The results showed that 33% of patients with PCOS were diagnosed with MBS; this was 11.7% in the control group (p<0.01). Adiponectin levels were significantly lower in PCOS patients with MBS than PCOS patients without MBS (p<0.001). After adjustment for body mass index (BMI), adiponectin levels were correlated negatively with waist circumference, triglycerides, diastolic blood pressure, homeostasis model assessment (HOMA) and positively with HDL. PCOS patients with adiponectin levels lower than median value had 10.5-fold higher risk of having MBS. Logistic regression analysis revealed that adiponectin levels were independently associated with the risk of having MBS, and the significance did not change after adjusting for each component of MBS. We concluded that patients with PCOS had an increased prevalence of MBS and thus an increased risk of cardiovascular disease. Hypoadiponectinemia was independently associated with MBS in these patients. Adiponectin as an endogenous biologically relevant modulator of vascular remodeling may have a role in the development of MBS in PCOS patients.