Background: More than one million children throughout the world are born by using fertility techniques. In this process, human intervention and laboratory conditions may have an impact on the growth and development of the fetus. Objectives: The present study aimed to consider the effect of assisted reproductive techniques on the results of embryonic health screening tests. Methods: In this case-control study, among clients who went to the Infertility Center of the Ome Leila Hospital in Bandar Abbas Province, we selected 200 pregnant women who were impregnated via assisted reproductive techniques as the case group and 200 natural pregnant women as the control group by sample random sampling. Checklists were filled out and data analyzed by the SPSS version 21 and chi-square tests by using an interview with pregnant women and investigating the embryonic screening tests. Results: Most of the participants in the study were housewives and had primary infertility. Their BMI was normal. There was no significant difference between the final results of the embryonic screening test in the two groups at the first trimester (P > 0.05). However, in the second trimester, there was a significant difference between them. The positive results were higher in the case group in comparison with the control group (P = 0.001). The mean of all types of screening tests in the first trimester in both groups was not different, significantly (P < 0.05), although in the second trimester, the mean of all the testis, including BHCG (P = 0.006) and AFP (P = 0.018) in both case and control groups, was significantly different. The mean of BHCG and AFP was higher in the case group, while the mean of Estradiol and Inhibin, NB, and NT were not really different (P < 0.05). Conclusions: Our study showed that embryonic screening tests, particularly the BHCG and AFP tests, would be affected by applying the assisted reproductive techniques. For the couples who had a history of infertility and used reproductive methods, screening tests are essential in the first and second trimester.