Polycystic ovary syndrome (PCOS) women are more insulin resistant than general population. Prevalence data on insulin resistance (IR) in PCOS vary depending on population characteristics and methodology used. The objectives of this study were to investigate whether IR in PCOS is exclusively associated with body mass and to assess the prevalence of IR in lean and overweight/obese PCOS. Study included 250 consecutive women who attended a Department of Human Reproduction diagnosed as having PCOS according to the Rotterdam criteria. Control group comprised 500 healthy women referred for male factor infertility evaluation during the same period as the PCOS women. PCOS women (n = 250) were more insulin resistant than controls (n = 500) even after adjustment for age and body mass index (BMI) (P = 0.03). Using logistic regression analysis, BMI ≥ 25 kg/m(2) (OR 6.0; 95 % CI 3.3-11.0), PCOS (OR 2.2; 95 % CI 1.4-3.5) and waist circumference ≥ 80 cm (OR 2.0; 95 % CI 1.1-3.8) were identified as independent determinants of IR (P < 0.001). IR was more prevalent in overweight/obese controls (n = 100) than in lean PCOS women (n = 150), 31 versus 9.3 %, but less prevalent than in overweight/obese PCOS (n = 100), 31 versus 57 %. The prevalence of IR between lean controls (5 %) and lean PCOS (9.3 %) did not significantly differ. Both PCOS-specific and obesity-related IR independently contribute to IR in PCOS. Using HOMA-IR cutoff value of 3.15 specific for Croatian women in our clinical setting, the assessed prevalence of IR in lean and overweight/obese PCOS women was 9.3 and 57 %, respectively.