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 frequency, describe the types and risk factors of congenital anomalies among newborns admitted to Neonatal Intensive Care Unit (NICU) of Assiut University Children's Hospital. Study design: It is a prospective observational study (analytic cross sectional study) was performed and screening of the newborns admitted at NICU of Assiut University Children's Hospital (for 6 months) during the period from 1^st December 2017 to 31^st May 2018. The sample included 346 newborns, 173 cases and 173 controls. We collected data using a record checklist and an interviewing questionnaire.Results: There were significant differences between cases and controls 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 and 1Conjoined Twins) 23 cases (13.3%) followed by cardiovascular anomalies 22 cases (12.7%), followed by CNS anomalies 18 cases (10%). Conclusions: The frequency of congenital anomalies was 22.97%. The most common anomalies were gastrointestinal anomalies (GIT), musculoskeletal anomalies, multiple anomalies and cardiovascular system anomalies. The risk factors were consanguineous marriage, positive family history, urban areas, full-term and singleton pregnancies.