Abstract Background: Congenital malformations are a major cause of infant impairment and mortality, especially during the neonatal period, and constitute a significant and growing clinical and public-health challenge, due to the impact on the health of the population. In the world, it is estimated that 2 to 5% of newborns have some type of malformation and about 303,000 die during the neonatal period. In many low- and medium-income countries, congenital malformations are not considered a public health priority and are perceived by the medical community as rare and unavoidable events. Objectives: to assess the clinical patterns of congenital malformations among neonates admitted in HUCSH NICU from December 2019 to January 1st 2022 G.C. Methods: Institutional based retrospective cross sectional design study by reviewing charts of neonates admitted from December 2019 to January 2021was used. There were about 2020 new born admissions in HUCSH neonatal ward, sample size was calculated by using the standard formula making 354 new borns was selected but 313 newborn chart was assessed, due to incomplete chart and lost chart with response rate of 96 5 %. Data will be collected by using structured tools and analyzed by using SPSS version 20 and association will be analyzed by using bivariate and multivariate regression technique Result: out of 313 newborn chart assessed, the magnitude of CM was 11.8%, Neural tube defect accounts 32% followed by ARM, and HSD.68% of newborns with congenital malformation underwent surgery among those 28.6% of them were dead while they were in hospital. Mothers who had 1 previous abortion has 4.7% (AOR:0.047 95 CI[.013,.176] increased risk of giving a baby with congenital malformation than who had no abortion history. The likelihood of having congenital malformation of among newborns born from mother who started folate supplementation after the first trimester of pregnancy had 17.5% higher increased risk with (AOR:0.175 95 CI[.035,.872]) than who were supplemented before conception. Conclusion: The magnitude of congenital malformations was higher stated in this study. So generally, this study was done among only neonates admitted to NICU, so the result would be expected to be higher,it might not generalize the true magnitude of congenital malformation in the population