Background: Congenital anomalies are considered as one of the major causes of neonatal death. The prevalent pattern of congenital anomalies may vary diachronically or geographically. With regard to the pervasiveness of under-five mortality (probability of dying between birth and exactly 5 years old) in Hamadan province in the recent years, the present study intended to determine the risk factors of congenital anomalies of newborns in Hamadan province in 2017. Methods: The present case-control study was conducted in the hospitals affiliated to Hamadan University of Medical Sciences for 6 months in 2017. The study targeted all the newborns from birth to hospital discharge. The neonatal cases with congenital anomalies were identified through clinical examination. A report sheet was assigned to a healthy newborn, as a control, per each case of congenital anomalies born on the same day and in the same hospital. Once data was collected, they were statistically analyzed by means of SPSS V. 16 software. Results: According to the current results, the prevalence of congenital anomalies was 0.85% (8.5 per 1,000 live births). Genitourinary (40%), musculoskeletal (25.2%), eye, ear and neck (18.5%), chromosomal (5.9%), respiratory tract (3.7%) and cardiovascular system (2.2%) were the most common congenital anomalies, respectively. Consanguineous marriage, concomitant use of contraceptive methods and male sex were found to be the most important risk factors for congenital anomalies. Conclusions: The present study aimed at identifying the various types and prevalence of congenital anomalies in Hamadan province. Regular prenatal examination and early diagnosis for prevention, early intervention and scheduled termination of pregnancy are recommended. Besides, public awareness of the disadvantages of consanguineous marriage and other pertaining risk factors affecting the incidence of congenital anomalies is also recommended.