Abstract: Misoprostol is a cheap product of prostaglandin E1 which has gained interest in pregnancy termination. The aim of this study was to compare the effect of vaginal misoprostol and prostaglandin E2 suppository in pregnancy termination before 20 weeks of gestational age. In this clinical trial, 111 participants under 20 weeks of gestational age who needed pregnancy termination were enrolled. They were divided into two groups misoprostol and prostaglandine E2 treatment. Fifty four people received vaginal misoprostol as 25 μg per 4 h up to 3 days and 57 participants received prostaglandine E2 vaginal suppositories. Data were analyzed using SPSS software. Mean age of participants was 27.5 years and its standard deviation was 6.1 years. Mean gestational age was 13.1 weeks based on sonographic measurement and it was 14.5 weeks by LMP estimation. Mean induction to evacuation time was 3.1 days and in misoprostol group was 2.4±0.88 days. Half of the patients in control group and 70% of them in misoprostol group succeeded pregnancy termination in 48 h. Vaginal misoprostol compared to prostaglandine E2 vaginal suppository has higher efficacy in shorter time.