Background Small intestinal atresia (SIA) is a congenital anomaly characterised by the abnormal closure, discontinuity or narrowing of the duodenum, jejunum or ileum. This study aimed to describe the epidemiology of SIA in Europe.

Methods SIA cases delivered during 1990–2006 and notified to 21 European congenital anomaly registers formed this population-based case series. Risk of spontaneous fetal loss, accounting for terminations, was examined by Cox regression. Age-adjusted prevalence was modelled using multilevel Poisson regression.

Results 1154 SIA cases were reported among 5 383 099 births. Of 1092 singleton cases, 222 (20.3%) were associated with chromosomal and 227 (20.8%) with structural anomalies. Chromosomal and structural anomalies occurred more frequently in duodenal atresia than jejunoileal atresia (JIA) (p<0.001 for both). The prevalence for singleton cases of normal karyotype was 1.6 per 10,000 births (95% CI: 1.5 to 1.7) for SIA, 0.9 (95% CI: 0.8 to 1.0) for duodenal atresia and 0.8 (95% CI: 0.7 to 0.8) for JIA. Of the singleton cases of normal karyotype, 91.4% resulted in live birth, 4.3% in spontaneous fetal loss (≤20 weeks gestation) and 4.4% in termination of pregnancy. The risk of spontaneous fetal loss was 6.2% for SIA, varying significantly between 9.4% for duodenal atresia and 2.4% for JIA (p<0.001). There was no evidence of an increased risk of SIA in mothers aged ≤20 years compared to mothers aged 20 to 29 (relative risk=1.3, 95% credible interval: 1.0 to 1.8; p=0.08).

Conclusion Chromosomal and structural anomalies are more common, and the risk of fetal loss greater, in cases of duodenal atresia compared to JIA.