Poly Cystic Ovary Syndrome (PCOS) is mainly characterised by reproductive hormonal imbalance and increased androgen levels, ovulatory dysfunction and polycystic appearing ovaries on ultrasonography. The obesity is common factor to cause PCOS and this adipocytokines play an important role to cause obesity related disorders. Hence, the present study aimed to evaluate the role of adiponectin in women with PCOS compared them with healthy controls. This case control study included total eighty (80) subjects out of this fourty subjects with PCOS and remaining fourty (40) age and body mass index matched healthy controls. The fasting, post parandial blood sugars, glycated haemoglobin, lipid profile and adiponectin levels were measured and data was recorded. There was a significantly elevated levels of total cholesterol, triacylglycerol, very low density lipoprotein, low density lipoprotein (p = 0.0001**) and there were no significant levels of fasting and post parandial blood sugars, glycated haemoglobin levels were observed in women with PCOS than in controls. Additionally, we also observed significantly decreased levels of high density lipoprotein and adiponectin in women with PCOS when compared to healthy controls (p = 0.0001**). The adiponectin shown a positive correlation with age, high density lipoprotein and negative correlation with total cholesterol, triacylglycerol, very low density lipoprotein and low density lipoprotein (p = 0.0001**). The altered adiponectin levels in polycystic ovary syndrome appear to form an important link between obesity and the complications of PCOS.