© Springer-Verlag 2012.Objective Polycystic ovary syndrome (PCOS) is described as a low-grade chronic inflammatory state where the macrophage infiltration increased in visceral fat play the major role. The aim of this study was to assess chitotriosidase (ChT) activity (an activated macrophage marker) in women with PCOS and controls and to evaluate its correlation with anthropometric and biochemical parameters. Study design Seventy-nine women with PCOS and 60 healthy controls were included in the study. PCOS and controls were divided into two subgroups according to body mass indexes (BMIs) as normoweight (<25 kg/m2) and overweight (≥25 kg/m2). ChT activity, biochemical (free testosterone, luteinizing hormone, insulin resistance index, etc.) and clinical parameters [BMI, waist-to-hip ratio, modified Ferriman–Gallwey scores (mFG)] were analyzed according to groups. Results Serum ChT activity was significantly (p < 0.001) higher in women with PCOS than controls (normoweight, 87.1 ± 90.1 vs. 18.4 ± 9.0 nmol/ml/h; overweight, 92.0 ± 96.7 vs. 17.9 ± 12.1 nmol/ml/h PCOS and controls, respectively). No statistically significant difference was noted between ChT activity of normoweight and overweight PCOS subgroups. A positive correlation was found between ChT activity and PCOS status (r 0.598, p < 0.001), mFG scores (r 0.525, p < 0.001), free testosterone (r 0.402, p 0.001) and total testosterone (r 0.168, p 0.048) for the combined groups (PCOS + controls). In multivariant linear regression analysis participants’ PCOS status (presence or absence) and LH levels were the main predictors of ChT activity in the whole study population (p 0.002 and p0.041, respectively). Conclusion ChT activity elevates in PCOS independent of obesity. Our findings support the concept of PCOS is a state of low-grade chronic inflammation where the macrophages could play the major role. Hyperandrogenism might also be related to this inflammatory state and can be a subject of further trials.