Mercaptopurines, including azathioprine and 6-mercaptopurine, are commonly used as immunosuppressive agents to induce and maintain remission of Crohn’s disease. This class of drugs has been assigned a risk level of (D) for pregnancy by the U.S. Food and Drug Safety Administration (FDA) and is therefore considered potentially harmful to the fetus. The study showed that: (1) in male patients, there is no increased risk of fetal malformation when mercaptopurine drugs are taken during pregnancy attempts. (2) In female patients, the use of mercaptopurines during pregnancy or the first trimester did not affect fetal weight or increase the risk of congenital malformations, but did increase the risk of preterm delivery. Summary: Fertility has always been a common concern for both the treating physician and the patient with Crohn’s disease. Medications during pregnancy have an impact on the conception of a healthy fetus; therefore, pregnant patients should actively communicate with their treating physician when choosing medications and adjust their medication regimen according to their condition.