Introduction: Congenital anomalies are one of the important causes of disability and infant mortality. These abnormalities occur during egg fertilization or embryonic development, which can be detected by laboratory methods. The aim of this study is to investigate the prevalence of congenital anomalies in Rafsanjan City. Methods: This cross-sectional study was performed on 4868 infants born in Rafsanjan city in 2018. Data collection tool was a questionnaire including information about mothers and infants. The questionnaire was completed using health records available in health centers of Rafsanjan city. Data were analyzed using SPSS 20 and independent t-test and Chi-square. Results: The results showed that the overall prevalence of congenital anomalies in Rafsanjan was 5/38 per 1000 live births. Out of 4868 pregnant women, 474 (9/7%), had abortions or stillbirths before the second trimester, and 12 (0/2%) had therapeutic abortions. After analyzing these anomalies, three cases of Down syndrome (trisomy 21), three cases of Edward syndrome (trisomy 18), one case of aneuploidy, and two cases of microcephaly were found, and the rest had one of the structural abnormalities. . Conclusion: The results of this study indicated a high rate of congenital anomalies in Rafsanjan. Therefore, further studies are recommended to better understand the causes and prevent these anomalies.