Background: Congenital malformations (CMs) are structural and functional anomalies that have a significant but under-recognized cause of mortality and morbidity among infants and children under 5 years of age. CMs are not only life threatening, but also result in long-term disabilities that negatively affect individuals, families, health care systems and societies.

Objectives: The purpose of this study was to describe the prevalence and outcomes of birth defects in newborns of South Wollo and Oromia zones of Amhara regional state.

Methods: A retrospective cross-sectional study was done in three hospitals of South Wollo and Oromia zones, where 22,624 infants were born between January 2015 and December 2017. The presence and type of birth defects in the infants, as well as their outcomes, were identified by reviewing the medical records of their mothers. Medical records with incomplete information were excluded from the study. The data were collected using a pre-tested checklist for data collection.

Results: A total of 22,624 infants were born during the study period. Three hundred and twenty-four (1.43%) newborns were delivered with birth defects. Anomalies of the central nervous system (CNS) were the most frequent type of birth defect (43.2%), followed by defects of the musculoskeletal system (19.7%), orofacial malformations (11.0%) and gastrointestinal system anomalies (6.1%). Most of the malformed infants were born from mothers with a history of alcohol intake (55.8%), lack of iron and folic acid supplementation (58.4%), family history of birth defects (58.7%) and history of diseases during pregnancy (53.5%). The outcomes of newborns with birth defects were significantly affected by the type of birth defect, gestational age, weight of the newborn and presence of twin pregnancy (p-value ≤0.05).

Conclusions: The prevalence of CNS anomalies was the highest, followed by musculoskeletal system anomalies. The type of birth defect, gestational age, weight of newborn and twin pregnancy significantly affected outcomes of the newborns with congenital anomalies. Therefore, in order to reduce the prevalence of CMs, the identification and management of risk factors should be the focus of stakeholders.