Background Congenital anomalies play a significant role in perinatal mortality. Congenital anomalies are a cause of death in a third of all babies that die in the first year of life in Latvia.

Methods The Register of Newborns was used to identify all babies born 2000–2007 and who were diagnosed with a congenital anomaly (Q00-Q99). HRs with 95% CI were estimated using Cox regression model adjusted for mother's age, newborns' gender, different complications during deliveries and pregnancies, gestational time, newborns' birth weight and antenatal care factors.

Results Congenital malformations of the circulatory system were diagnosed in 41.9% (95% CI 32.7% to 51.7%) of all babies that died in the first year of life; 13.2% (95% CI 7.8% to 21.2%) had musculoskeletal malformations. Multiple anomalies and serious anomalies, such as diaphragmatic hernia and malformations of the digestive system were found in 7.9% (95% CI 4.1% to 14.9%). The risk of death in newborns with congenital malformations of the circulatory system was greater in mothers aged 20–34 years compared to mothers under 19 years of age (HR 5.64 95% CI 1.65 to 19.27; p=0.01) and in babies with low birth weight (HR 3.09; 95% CI 1.27 to 7.51). For digestive system anomalies mortality was associated with complications during pregnancy (HR 1.67; 95% CI 1.11 to 2.52; p=0.01). For musculoskeletal system malformations mother's disease in pregnancy (HR 11.04; 95% CI 1.31 to 9.30; p=0.03) and complications during delivery (HR 18.98; 95% CI 2.39 to 15.04; p=0.00) were associated with mortality.

Conclusions The risk factors identified highlight the importance of careful antenatal care.