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Abstract Background : Intrauterine development can be considered as normal development as well as abnormal development. Abnormal development commonly called birth defects occur because of interference of normal development from genetic disorders, environmental factors and the combination of both genetic and environment factors during the critical period of embryogenesis. The present study aimed to evaluate the prevalence and patterns of birth defects at birth in Southwestern Ethiopia. Methods : Institutions based cross-sectional study design was used. Six hospitals were selected from the existing hospitals in southwestern Ethiopia purposively based on case load. The study was conducted from September 2011 to December 2015 during which 45,951 deliveries were attained. All records of births that were occurred in the selected hospitals during the study period were identified from medical records, to locate the birth defect records.Results : Twenty-one different birth defects were recorded. Of these, 49.6 % of the birth defects recorded were Anencephaly and Hydrocephalus. Five types of birth defects namely: Anencephaly (25.0%), Hydrocephalus (24.6%), Spinal bifida (13.1%), Meningomyelocele (7.1%), and Umbilical hernia (4.8 %) accounted about three-fourth (75%) of all recorded birth defects. The present study revealed that the prevalence of the birth defects at birth was found to be 5.5 per 1000 births. Among twenty one birth defects identified in this study, the neural tube defects were the most frequent with prevalence rate of 4.1 per 1000 birth followed by gastrointestinal defects (0.7 per 1000 births)Conclusions: As compared to other study, the prevalence of birth defect identified in the present study was found to be higher. The neural tube defects were the most prevalent with the frequency of 4.05 cases per 1000.The present study also identified that nearly equal proportions of birth defect occurred among males and females newborns. The majority of the mother who gave birth to birth defects was younger than 35 years old. As the birth defect was found to be a main cases of infant mortality and morbidity, there need to an urgent interventions to control the cases.