This study investigated the influence of metformin and rosiglitazone on ovarian and endometrium of polycystic ovarian syndrome patients. Forty-four women were chosen by simple random sampling from referred women to obstetrics and gynecology clinic of Al-Zahra and Shahid Beheshiti Hospitals, Isfahan, Iran. The study consisted of a 6-week baseline observation period, a 12-weeks treatment period of single-agent therapy (rosiglitazone or metformin), and then a 12-weeks period of combined therapy. Repeated measure analysis showed that there was significant difference between measurements of waist, TG, hirsutism, FBS and testosterone in both treatment groups over thirty weeks (all p-values < 0.05). Ovary size was statistically different in metformin group in three measured time (p-value < 0.001). Also number of follicles (p-value= 1 and 0.564) and follicle size (p-value= 1 and 1) were not different in three phases of study in metformin and rosiglitazone groups according to Wilcoxon signed ranks test. It was concluded that there was significant change in waist, TG, hirsutism, FBS, testosterone and insulin resistance over thirty weeks in each of metformine and rosiglitazon groups but there was not statistical difference in HDL and BMI. Testosterone level after single therapy and combination therapy in rosiglitazone reduced more significantly than metformin group. On the other hand, ovary size decreased more in metformin group after single therapy and combination therapy than rosiglitazone.
