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Background: Globally, 240,000 babies die in the neonatal period annually due to congenital anomalies (CA). Malta reports the highest neonatal mortality rate (NMR) among EU (European Union) Countries, constituting a public health concern. Objectives: This study describes the contribution of CA to NMR in Malta, investigating possible associations with known maternal risk factors of maternal age, nationality, and education. Additionally, it provides an update on the contribution of CA to neonatal deaths in Malta and other EU countries. Methods: Anonymous data for births and neonatal deaths were obtained for 2006–2020 from the National Obstetrics Information System (NOIS) in Malta. Regression analyses adjusting for maternal risk factors were run on this data to explore possible associations with NMR. NMRs published by EUROSTAT 2011–2020 were used to compare mortality by underlying cause of death (CA or non‐CA causes) for Malta and other EU countries. Results: Between 2006 and 2020, 63,890 live births with 283 neonatal deaths were registered in Malta, (NMR 4.4 per 1000 live births). CA accounted for 39.6% of neonatal deaths. No time trends were observed in either total NMR, NMR attributed to CA or mortality due to non‐CA causes. Adjusted variables revealed associations for women hailing from non‐EU, low‐income countries. Malta registered high NMRs compared to EU countries, most marked for deaths attributed to CA. Conclusions: Between 2006 and 2020, Malta's NMR remained stable. Maternal Nationality, from non‐EU low‐income countries, was associated with higher neonatal mortality. The influx of such migrants may play a partial role in the high NMRs experienced. Malta's high NMR was primarily driven by early neonatal deaths, which included high proportions of deaths due to CA and is linked to the fact that termination of pregnancy is illegal in Malta. [ABSTRACT FROM AUTHOR]