Background: Congenital anomalies (CA) are common causes of infant’s and childhood deaths and disability. Objectives: The aim of the study is to determine the prevalence, describe the types and risk factors of congenital anomalies among newborns admitted to Neonatal Intensive Care Unit (NICU) of a Children's Hospital. Study design: It is a prospective observational study(analytic cross sectional study) was performed and screening of the newborn admitted at NICU of a Children's Hospital during the period of 6 months from 1 to 12-2017 to the end of 5-2018. The sample was 346 newborns, 173 cases and 173 control. We collected data using a record checklist and an interviewing questionnaire.Results: There were a significant difference between cases and control concerning gestational age (P=0.001), single or multiple babies (P=0.002), residence (P=0.001), consanguineous marriage (P=0.01) and family history of unfavorable outcome (P=0.001). We also found that the most common type of congenital anomalies was gastrointestinal anomalies 63 cases (36.4%) with tracheoesophageal fistula 17 cases (27%) being the most common GIT anomalies. Then the musculoskeletal anomalies being the second common anomalies 14.5% with diaphragmatic hernia 10 cases being the most common in musculoskeletal anomalies followed by other anomalies (22 multiple +1Conjoined Twins 23 cases (13.3%) followed by circulatory anomalies 22 cases (12.7%), followed by CNS anomalies 18 cases (10%). Conclusion: The prevalence of congenital anomalies was 22.97%. The most common anomalies were gastrointestinal anomalies (GIT), musculoskeletal anomalies, multiple anomalies and circulatory system anomalies. The risk factors were consanguineous marriage, positive family history, urban areas, full-term and singleton pregnancies.