Background: Congenital hypothyroidism (CH), as one of the most common congenital endocrine disorders, may be significantly associated with congenital malformations. This study investigates urogenital abnormalities in children with primary CH (PCH). Methods: This case-control study was conducted on 200 children aged three months to 1 year, referred to Amir-Kabir Hospital, Arak, Iran. One hundred children with PCH, as the case group, and 100 healthy children, as the control group, were selected using convenient sampling. For all children, demographic data checklists were filled, and physical examination, abdomen and pelvic ultrasound and other diagnostic measures (if necessary) were performed to evaluate the congenital urogenital abnormalities including anomalies of the penis and urethra, and disorders and anomalies of the scrotal contents. Results: Among 92 (100%) urogenital anomalies diagnosed, highest frequencies with 37 (40.2%), 26(28.2%) and 9 (9.7%) cases including hypospadias, Cryptorchidism, and hydrocele, respectively. The frequency of urogenital abnormalities among 32 children with PCH, with 52 cases (56.5%) was significantly higher than the frequency of abnormalities among the 21 children in the control group, with 40 cases (43.4%). (OR=2.04; 95%CI: 1.1-3.6; p=0.014). Conclusion: Our study demonstrated that PCH is significantly associated with the congenital urogenital abnormalities. However, due to the lack of evidence in this area, further studies are recommended to determine the necessity of conducting screening programs for abnormalities of the urogenital system in children with CH at birth.