Polycystic ovary syndrome (PCOS) is the most common endocrine disease in fertile women. It is also closely associated with insulin resistance (IR). The purpose of this trial was to investigate the value of clinical and laboratory IR markers routinely used in type 2 diabetes patients (DM2) for the diagnosis of IR in PCOS patients. The goal was to identify the most suitable marker for this condition out of the entire tested panel, which was comprised of HOMAIR intact proinsulin (IP), Sib index and IRIS II score. A total of 50 women with PCOS were recruited, along with 20 comparable, healthy women for the control group. HOMAIR values indicating IR (>2) were seen in 26 patients (52%). Patients with IR (based on HOMAIR) had significantly higher values for BMI (p< 0.001), fasting glucose (4.7 ±0.6 vs. 4.2±0.3mmol/l, p = 0.001), insulin (16.8 ±6.2 vs. 7.1 ±2.1 pU/ml, p< 0.001), IP (3.2 ±2.0 vs. 1.8 ± 1.0pmol/l, p = 0.004), triglycerides (1.16 ±0.77 vs. 0.80± 0.35 mmol/l, p = 0.04), Sib index (6.65 ±2.61 vs. 1.7 ±11.36, p< 0.001) and IRIS II score (24 ±19 vs. 11 ±11, p = 0.008). A comparison between the control group and PCOS patients with IR and IS showed significant differences in BMI (p<0.001), triglycerides (p = 0.048), HDL (p< 0.001), fasting glucose (p = 0.004), insulin (p<0.001), IP (p = 0.001), HOMAir (p< 0.001), IRIS II score (p = 0.003) and Sib index (p< 0.001). The results of this study indicate that our patients with PCOS did not reach a level of IR that would result in higher IP secretion instead of insulin secretion. Out of the entire tested panel, HOMAIR score and Sib appeared to be the most suitable markers to assess IR in our patient population. IRIS II score was less sensitive than HOMAIR or Sib. None of the patients reached the required IRIS II threshold in DM2 for IR either. Therefore, HOMAIR and Sib may be suitable indexes for the diagnosis and therapeutic monitoring of IR in this specific patient population.