Introduction Congenital anomalies are structural abnormalities, which are diagnosed antenatally, at birth or within the first few years of life. Knowledge of the prevalence of congenital malformations and their trend is crucial to identifying new potential causative and preventative factors and also in the provision of adequate services for patients affected by congenital anomalies.

Objective The objective of this research is to provide a cohesive analysis of the EUROCAT Cork/Kerry congenital anomaly data from 1996 to 2010, focusing on baseline epidemiological information and certain maternal variables.

Methods This was a retrospective study of all recorded cases of congenital anomalies in Cork and Kerry from 1996 to 2010 using the EUROCAT Cork and Kerry database and baseline epidemiological data from the Central Statistics Office.

Results There was a higher prevalence in overall and live birth prevalence in Cork and Kerry from 1996–2010 in comparison to EUROCAT data. The overall prevalence of congenital anomalies was 25.97 /1000 births in Cork and Kerry during this period versus 23.8 in EUROCAT. Livebirth prevalence’s were 24.72/1000 births versus 19.93 EUROCAT prevalence. Higher prevalences were noted for anomalies of the respiratory, eye and ear subgroups and for Down syndrome and congenital heart disease.

Conclusions Higher rates of congenital anomalies were seen in the Cork and Kerry registry overall than in the European database. This may be due to actual higher numbers of cases but there are a number of other possible reasons. A further in-depth analysis of the registry may yield additional information.