A congenital malformation (CM) or birth defect is a structural or functional abnormality observed in children. CMs occur during intrauterine development of embryo or fetus. It may be visible before birth, at birth or later in life, and are major causes of children’s hospital admissions and deaths. The aim of this study was to assess the prevalence and the associated risk factors of CMs in Bair Dar and Gondar, Ethiopia. An institution-based, retrospective cross-sectional study was conducted in four governmental hospitals where 61,934 infants were born from September 2015 to December 2019. Among these, 736 (1.2%) infants were born with CMs, and the types of CMs were identified. To identify associated risk factors, maternal medical history books of all CM positive (736) and 681 CM negative newborns (736+681=1417) were consulted. The data were collected using a semistructured checklist. The most frequent types of CMs were neural tube defects (39.7%), followed by Oro-facial clefts (23.6%), cardiovascular system defects (10.3%) and Down syndrome (7.1%). Lack of folic acid supplementation (AOR=9.79, 95% CI: 6.89-13.92), presence of chronic disease (AOR=3.25, 95% CI: 2.29-4.60), intake of drugs (AOR=19.93, 95% CI: 13.5-29.3), consumption of alcohol during pregnancy (AOR=1.64, 95% CI: 1.17-2.29) and maternal age (AOR=4.62, 95% CI: 3.24-6.58) were significantly associated with birth defects. These findings suggest that there is an increasing burden of CMs in Bahir Dar and Gondar, Ethiopia. The findings reflect that sustainable surveillance and registry systems are mandatory for intervention activities. In this respect, the current study might fill an important information gap on CMs in the study area. Further detailed, nationwide, multicenter, retrospective/prospective investigations should be conducted to influence policy and healthcare decision-making so as to reduce congenital malformations. Key words: Associated risk factors, Congenital malformations, Newborns, Prevalence