Abstract Background : A birth defect is a structural or functional abnormality observed in children. Birth defects occur during intrauterine development of embryo or fetus. Birth defects may be visible before birth, at birth or later in life, and are major causes of children’s hospital admissions and deaths. Objectives : The aim of this study was to assess the prevalence and identify the associated risk factors of birth defects. Method: A retrospective cross-sectional study was conducted in two referral hospitals where 19,650 infants were born between 2015 and 2017. Among these, 317 infants born with birth defects were selected, and the types of birth defect were identified. To identify associated risk factors, 321 maternal medical history books were selected by simple random sampling. The data were collected using a semi-structured checklist. Results: A total of 19,650 infants were delivered during the study period. Among these, 1.61% of the infants had birth defects. The most frequent types of birth defect were neural tube defects (32.5%), followed by oro-facial clefts (27.1%), cardiovascular system defects (12%) and upper and lower limb defects (8.8%). Lack of folic acid supplementation (95% CI: 3.54-12.08), presence of chronic disease (95% CI: 2.27-7.21), intake of drugs (95% CI: 1.98-6.38) and consumption of alcohol during pregnancy (95% CI: 1.13-3.60) were significantly associated with birth defects. Conclusion: The study identified a high prevalence of birth defects in infants born in Northwest Ethiopia. The most frequent type of birth defect was neural tube defect. In addition, the absence of maternal folic acid supplementation and the presence of chronic diseases during pregnancy were among the risk factors significantly associated with birth defects. Further detailed, nationwide, multicenter, retrospective/prospective follow up investigations should be conducted to influence political and healthcare decision-making so as to reduce birth defects. [Ethiop. J. Health Dev. 2018;32(3):00-000] Key words: Birth defects, prevalence, associated factors