Background Anti-Mullerian hormone (AMH) is expressed by granulosa cells of the pre-antral and small antral follicles in the ovary. Serum AMH levels are significantly higher in women with polycystic ovary syndrome (PCOS) due to an increased number of antral follicles and also a higher production per antral follicle. We proposed diagnostic criteria for the identification of PCOS that are based on variation in the AMH concentrations.Methods This study explored the relationship between serum AMH levels and other hormonal markers in patients with polycystic ovary syndrome (PCOS) and metabolic syndrome. One hundred fifty patients with PCOS and normally cycling women were examined in a cohort study. Of these, some were candidates for the assisted reproductive methods. The following serum levels were measured in all patients on day 5 of the menstrual cycle: AMH, glucose, HOMA/IP, BMI, testosterone and cholesterol, lipoproteins and triglycerides.Results In the PCOS group, a 2-fold increase in the serum AMH level was observed as compared to the controls. With AMH, the following increments were seen: testosterone (by 184%); fasting blood glucose (by 18%); fasting insulin (83.86%); HOMA/IR (by 64.23%); mean cholesterol (by 30%); mean triglycerides (by 17%); and BMI (by 26.75%). The high-density lipoprotein concentration decreased by 29.3%.Conclusion Thus, monitoring the level of AMH allows predicting for OHSS during the ovulation induction and during the use of assistive reproductive technologies. Such a practice also allows deciding on the treatment strategy for obesity, hirsutism, type II diabetes, infertility and cardiovascular diseases.