Pentraxin-3 (PTX3) a cytokine-inducible molecule is released from various tissues. Its level increases as a response to different inflammatory conditions. Polycystic Ovary Syndrome (PCOS) is considered as a proinflammatory state. The aim of this study was to investigate the association between PTX3 and various metabolic and hormonal parameters in PCOS patients. This study included 64 new diagnosed PCOS patients who had been never treated previously with PCOS and 46 healthy controls with matched age and body mass index (BMI). PTX3, biochemical and hormonal parameters of both groups were measured. The patients were divided into obese and nonobese subgroups according to BMI (above or lower than 25 kg/m(2)). PTX3, HOMA-IR and high sensitive C-reactive protein (hs-CRP) levels of these subgroups were compared. Serum PTX3 (p=0.013), hs-CRP (p=0.015) and HOMA-IR (p=0.023) levels of PCOS patients were significantly higher than the control group. Serum PTX3 has been found to have negative correlations with BMI (r=-0.318, p < 0.001), waist circumference (r=-0.306, p < 0.001), HOMA-IR (r=0.324, p < 0.001) and hs-CRP (r=-0.206, p=0.031). Subgroup analysis revealed PCOS women with obesity to have significantly higher serum PTX3 level than non-obese PCOS subjects (p=0.012), non-obese controls (p=0.015) and obese controls (p=0.002). Women with new diagnosed PCOS especially obese subjects had significantly lower serum PTX3 than the control group. PTX3 has been found to be negatively correlated with BMI and insulin resistance. Low PTX3 level may have a role in the etiology of PCOS and in the formation of atherosclerotic diseases by stimulation of chronic inflammation.