The aim of this study was to evaluate the ovarian cysts appearing during GnRH-a/hMG treatment in patients with polycystic ovarian syndrome (PCOS). A total of 35 women with PCOS were included in the study. All women received 3.75 mg IM of long-acting leuprolide acetate on the first day of the menstrual cycle. On the 15th day of the menstrual cycle, transvaginal ultrasound examination (US) and determination of serum E2 were done. A total of 90 cycles were studied in this way and during these cycles, 14 (15.5%) ovarian cysts with a diameter of ≥ 20 mm developed. According to the serum E2 levels, 11 cases (group A) had E2 concentrations > 35 pg/ml and 3 (group B) had serum E2 levels < 35 pg/ml. Group A patients attained a significantly larger mean size of ovarian cyst than group B patients (42 ± 7.3 vs. 24.2 ± 3.2 mm, p < 0.001). When the serum E2 concentrations were < 35 pg/ml, the ovarian cysts were disregarded and ovarian stimulation with gonadotropins was initiated. In case that serum E2 levels were > 35 pg/ml, the initiation of the ovarian stimulation with hMG was postponed until serum E2 levels indicated down-regulation, which was achieved after 5.8 ± 2.9 days. In both groups the ovarian stimulation resulted in ovulatory cycles, while four pregnancies in group A and one in group B were achieved. In conclusion, our results indicate that in patients with PCOS the GnRH-a administration may cause follicular cysts at an incidence of 15.5%. These cysts do not constitute a contraindication for ovarian stimulation provided that serum E2 levels are low.