Background: Several markers of low-grade chronic inflammation are altered in women with polycystic ovary syndrome (PCOS). Neopterin (NEO) is a marker of celullar immunity, and oxidative stress, mainly produced by activated macrophages. We aimed to evaluate the NEO levels in PCOS patients and correlate them with antropometric and biochemical parameters. Methods: The study groups consisted of 69 women with PCOS and 46 healthy controls. Both groups were divided into two subgroups according to their body mass index (BMI): <25 = normoweight, >25 = overweight. The clinical and biochemical parameters and serum NEO levels were analyzed. Results: Circulating levels of NEO were significantly (p < 0.001) higher in women with PCOS (normoweight: 15.9 ± 4.7 nmol/l; overweight 13.3 ± 8.1 nmol/l) compared to controls (normoweight: 8.6 ± 2.0 nmol/l; overweight 9.2 ± 1.8 nmol/l) regardless of their weight classes. Waist-to-hip ratio (WHR) (p < 0.05), free and total testosterone (p < 0.001) were significantly elevated in women with PCOS compared to controls after controlling for the effect of obesity. Conclusion: Circulating NEO level s are elevated in PCOS independent of body mass index supporting the suggestion of PCOS is a low-grade chronic inflammatory state. © 2012 Informa UK, Ltd.