The aim of this study was to compare the effects of Metformin and Acarbose accompanying Clomiphene on the successful ovulation induction in infertile women with polycystic ovary syndrome. This randomized double blind clinical trial study was performed on 60 women with polycystic ovary syndrome. Women were selected and randomly divided in two control and intervention groups. Intervention group received Acarbose 100 mg/day for 3 months. In the first, second, and third weeks, they received 1 tablet, 2 tablets, and 3 tablets per day respectively. In addition, they received 100 mg Clomiphene from third to seventh day of menstruation, during the 3 month treatment period. The control group received Metformin 500 mg/day for 3 months. In the first, second, and third weeks, they received 1 tablet, 2 tablets, and 3 tablets per day respectively. In addition, they received 100 mg Clomiphene from third to seventh day of menstruation, during the 3 month treatment period. All the subjects in both groups before and after the treatment were examined for hirsutism, acne, oral glucose tolerance test, serum triglycerides, cholesterol, LDL, HDL. Also, induction of ovulation was assessed by vaginal ultrasound. The Mean of BMI and fasting glucose tolerance test in Acarbose group was less than Metformin group (P = 0.05). The mean of triglycerides, LDL and HDL levels did not differ between the two groups after the intervention (P > 0.05). The mean of cholesterol levels were different in the two groups after the intervention (P = 0.04). Frequency of ovulation induction in those who received Acarbose (78.5%) was more than those who received Metformin (46.6) (P = 0.012). Comparing with Metformin, Acarbose accompanying Clomiphene was more effective in ovulation induction and decreasing body mass index in infertile women with polycystic ovary syndrome.