Annually, 7.9 million neonates in the world have developmental anomalies. Together with prematurity, they constitute the main causes of mortality during the first year of life in developed and developing countries. In Chile, the estimated prevalence is 3.9% of all live births. There are no reports on the prevalence of malformations in the Araucania Region. Objective: to estimate the prevalence of congenital malformations at birth in neonates hospitalized in a Neonatology Service. Patients and Method: cross-sectional study. Reference population: 54,241 live births at the Regional Hospital of Temuco over a 10-year period. Cases came from the neonatology hospital discharge database according to the ICD 10 classification, from January 1, 2009, to December 31, 2018. Descriptive and analytical statistics were performed with the STATA 15 software. Results: 949 neonates with one or more congenital malformations were identified. The overall prevalence of neonates with malformations was 1.7%, the most prevalent being ventricular septal defect 40.9 x 10,000 live newborns (LNB), atrial septal defect 21.5 x 10,000 LNB, cleft lip and palate 14.0 x 10,000 LNB, congenital hypertrophic cardiomyopathies 8.1 x 10,000 LNB, and congenital rectal atresia and stenosis or absence of the anus 7.9 x 10,000 LNB. Conclusions: the overall prevalence of malformations is similar to that reported for the country. When analyzing by type, we found significantly higher incidences than those reported in previous studies.