Objective This study investigates human cartilage glycoprotein-39 (YKL-40) levels in patients with polycystic ovary syndrome (PCOS) and controls, and tests their relationship with metabolic and hormonal parameters. Design Clinical study carried out in a university hospital in Tekirdag, Turkey. Patients Eighty-five women with PCOS and normal glucose tolerance (NGT) and twenty-five women with PCOS and abnormal glucose tolerance (AGT), diagnosed according to Rotterdam criteria, and fifty-nine healthy women. Measurements YKL-40 levels, fasting hormone levels and metabolic parameters were investigated in all subjects. Results We showed increased YKL-40 levels in women with PCOS compared to controls. (152.57 +/- 3.96 mu g/l vs 98.16 +/- 1.6 mu g/l, P < 0.000). YKL significantly correlated with BMI (r = 0.344; P < 0.000), 2-h glucose (r = 0.193; P = 0.012), HOMA-IR (r = 0.268; P < 0.000) and fasting insulin (r = 0.310; P < 0.000), but not with waist/hip ratio (r = 0.016; P = 0.832) and fasting glucose (r = 0.108; P = 0.832). When ROC curve analysis was used to analyse the suitability of YKL-40 to identify glucose intolerance in women with PCOS, area under curve for YKL-40 was found to be significant (AGT-PCOS: AUC 0.632, P = 0.046). Conclusion Plasma YKL-40 levels increased in patients with PCOS compared to healthy subjects. Moreover, there was a significant difference in YKL-40 levels between AGT-PCOS and NGT-PCOS subjects. Subsequently, we also found that YKL-40 levels above the cut-off point may help the clinician to predict abnormal glucose tolerance in patients with PCOS.