Introduction There are very few population-based data on congenital brain anomalies. The aim of this study is to provide estimates of associated anomalies, prevalence and clinical outcomes in pregnancies where a brain anomaly has been detected.

Methods Data on all cases with a confirmed brain anomaly notified to the Northern Congenital Abnormality Survey 2000-09, formed this population-based case-series. Higher ascertainment was achieved by contacting neuroradiologists for confirmation of cases. Cases associated with multiple pregnancies, teratogenic syndromes, associations and skull anomalies were excluded.

Results 470 cases were notified to NorCAS during the 10 years. 43 (9%) were associated with syndromes or microdeletions and 70 (15%) with chromosomal anomalies, of which 28 (40%) were with trisomy 13. There were 229 (49%) isolated brain anomalies giving a total prevalence of 7.3 (95% confidence interval (95%CI): 6.4-8.3) per 10,000 births. Termination of pregnancy occurred in 72 (31%) cases and fetal death in five. The live birth prevalence was 4.9 (95%CI: 4.1-5.7) per 10,000 live births. Hydrocephalus, cerebral cysts\schizencephaly, encephalocele and holprosencephaly were the most common with total prevalences of 2.0, 0.8, 0.7 and 0.7 per 10,000 births respectively. There was a male predominance (56%) overall and in most subgroups, except holoprosencephaly (41%).

Conclusion This study is the first register based study to describe the prevalence of congenital brain anomalies. We found an association with trisomy 13 and identified hydrocephalus as the most common isolated anomaly. This information will help inform prenatal counselling when a brain anomaly is diagnosed.