Birth defects, encountered frequently by pediatricians, are important causes of childhood morbidity and mortality. Birth defects can be classified according to their severity, pathogenic mechanism, or whether they are involving a single system or multiple systems. This hospital-based prospective descriptive study highlights the prevalence of Congenital Anomalies (CAs) in one year among live born neonates delivered in Zagazig University Hospital (Egypt). All women giving birth to viable babies were included. Demographic details, associated risk factors and the type of CAs in all babies were recorded. Diagnosis of CAs was based on clinical evaluation, radiographic examination, ultrasonography, echocardiography and chromosomal analysis of the newborn whenever recommended. The overall incidence of CAs among live born neonates was 2.5%, as most of the cases were referred to Zagazig University Hospital (Egypt) for delivery. The musculoskeletal system (23%) was the most commonly involved followed by the central nervous system (20.3%). Involvement of more than one system was observed in (28.6%) cases. Among maternal and fetal risk factors; parental consanguinity, maternal under nutrition and obesity, positive history of an anomaly in the family, low birth weight, and prematurity were significantly associated with higher frequency of CAs (P<0.05), with non-significant differences for maternal age and the sex of the neonates. The current study highlights the prevalence of congenital anomalies in one year in Zagazig University Hospital. It revealed a high prevalence of congenital anomalies in our locality and stressed the importance of carrying out a thorough clinical examination of all neonates at birth.