Freezing embryos is the best way to increase fertility for women with ovarian hyper-stimulation syndrome and women at risk for ovarian dysfunction. Due to the importance of freezing and pregnancy embryos, the present study was conducted to compare the fertility rate and the affecting factors following fresh embryos and frozen embryos in women treated with assisted reproductive techniques. In this study, 250 infertile women and IVF/ICSI candidates were studied. Embryos were used in fresh or frozen groups for transfer to the uterus. The expression of the caspase-3 gene was also examined for further evaluation. Data analysis was performed using SPSS 16 software, Chi-square, independent t-test, and Kruskal-Wallis tests. Out of 250 infertile women, 96 (38.4%) became pregnant, of which 54 were in the fresh embryo group and 42 were in the frozen embryo group, which was not statistically significant (P=0.32). Infertility causes, number of embryonic cells and grading of transferred embryos, delivery complications, embryo implantation methods, number of produced embryos after delivery, and endometrial thickness were not significantly different between the two groups (P=0.53). The difference between the mean number of transferred embryos in the two groups was significant (P<0.05), which was no longer significant after excluding non-pregnant women, and in comparing with only pregnant women (P=0.36). The result of caspase-3 gene expression showed that there was significant differences between fresh embryos, healthy thawed frozen embryos, and destroyed thawed frozen embryos. But these results were totally different from the results of the Pregnancy rate section. Therefore, it is inferred that although caspase-3 genes are expressed in frozen embryos after thawing and are ready to destroy the embryo, there are probably a number of involved factors that prevent the activity of caspase-3 and do not allow the apoptotic process to occur. What these factors are and how they prevent this process needs further study.