We investigated the association between polycystic ovarian syndrome, dyslipidemia and glucose intolerance in a cross sectional analysis comparing 50 patients with polycystic ovary syndrome and 50 patients without the disease (control group) who were attending the Infertility clinic. Variables of interest were their body-mass index (Kg/m2), fasting and blood glucose levels after a 75 gram oral glucose tolerance test and their total cholesterol (mmol/L), total triglycerides (mmol/L), high density cholesterol lipoprotein (HDL) cholesterol (mmol/L) and, low density lipoprotein cholesterol (mmol/L) levels. Except for HDL where significantly lower values were observed, significantly higher levels were detected in patients with PCOS than that of the control group. The difference persisted even when the obesity index were adjusted and matched. We conclude that both glucose intolerance and dyslipidemia were significantly associated with PCOS irrespective of the obesity index.