Background: The prenatal prevalence of congenital anomalies in Iraq is still under debate because of deficiencies in diagnostic capabilities and low reliability of medical registration. Early antenatal diagnosis of fetal defects is important for early counseling, intervention and possible fetal therapy. Objectives: The aim of this study was to estimate prenatal frequency of major congenital anomalies and malformation patterns diagnosed by ultrasound in Fallujah city. Patients and Methods: A cross-sectional study using the recorded data of antenatal diagnosis of major fetal congenital anomalies conducted in Fallujah Hospital—Fetal Medicine Clinic for a period of 20 months (January 2012 to August 2013). During this period one or more obstetrical ultrasound examinations were performed for 2120 pregnant ladies. Results: A total of 178 cases with obvious fetal anomalies were diagnosed. The prenatal prevalence of congenital anomalies was 84 per 1000. The median maternal age at diagnosis was 29 ± 6.3 years. The mean gestational age at diagnosis was 27 weeks ± 5 days. Extremities and urinary system anomalies were the most frequently detected anomalies. Conclusion: The prevalence of structural fetal malformation diagnosed by ultrasound in Fallujah city is obviously higher than internationally reported figures.