Purpose: Megacystis Microcolon Intestinal Hypoperistalsis Syndrome (MMIHS) is a congenital and lethal disease, and the etiology of the disease is not clear. It is speculated that maternal ingestion of some drugs during pregnancy may be an etiologic factor. In this study we aimed to investigate the effect of maternal ingestion of clomiphene on fetal bladder and colon in pregnant rats. Methods: We separated animals into a control group including 14 rats and a clomiphene group with 30 rats. Nothing was given to the control group during pregnancy. Two mg/kg/day clomiphene intraperitoneally was given to the study group from the 6th to 12th day of pregnancy. All of them were sacrified on the 20th day of pregnancy. Histopathological examination of the fetal colon and bladder was performed. Results: In the clomiphene group a significant decrease in the thickness of the bladder wall, an increase in bladder epithelium, an increase in muscle atrophy of the colon and bladder wall, an increase in vacuoler degeneration of the muscles of the bladder and colon wall, a decrease in ganglion cell numbers in the myenteric plexus of the bladder and a decrease in the thickness of the bladder tunica muscularis were determined. Conclusion: In our rat model we found histological structural changes in the rats' colon and bladder walls as a result of using clomiphene on days 6-12 of pregnancy; a similar pathological finding to those found in some of the MMIHS patients' colons and bladders.