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ABSTRACT Objective The aim of the present study was to determine the prevalence of metabolic syndrome (MS) in infertile Iranian women with polycystic ovary syndrome (PCOS) using the ATPIII criteria. Subjects and methods In this cross-sectional study, 624 women with PCOS were enrolled at a tertiary referral center in Tehran, Iran, between April, 2012 and March, 2013. Diagnosis of MS was according to ATPIII criteria. Also, we divided PCOS patients into following two main groups: (i) with MS (n = 123) and (ii) without MS (n = 501), and then compared variables between two groups. Results The mean age, body mass index (BMI) and waist circumference were 28.6 ± 4.3 years, 26.7 ± 3.7 kg/m2 and 85.2 ± 8.7 cm, respectively. The prevalence of MS was 19.7%. Our findings showed that age, BMI, waist circumference and all metabolic parameters were higher in PCOS women with MS than related values in those without MS. The most and least prevalent forms of MS were low level of high density lipoprotein-cholesterol (HDL-C) and hypertension, respectively. Conclusion It seems the prevalence of metabolic syndrome in our country isn’t as high as western countries. The prevalence rate of MS increased with age and BMI. One of the major cardiovascular risk factors, low level of HDL-C, is the most prevalent metabolic abnormality in our participants.