Introduction Small intestinal atresia (SIA) is a congenital anomaly characterised by the abnormal closure, discontinuity or narrowing of the duodenum, jejunum or ileum. This study used multilevel regression to examine the total prevalence and temporal trends in the prevalence of SIA in Europe.

Methods Cases of SIA delivered during 1990–2006 and notified to 21 European congenital anomaly registers formed this population-based case series. Total prevalence and changes in prevalence over time were modelled using multilevel Poisson regression. Heterogeneity between registers was evaluated from the intercept's random component. Inter-regional differences in trends were examined by including random slopes.

Results 1154 SIA cases were reported among 5 383 099 registered births. Of 1092 singleton cases, 222 (20.3%) were associated with chromosomal and 227 (20.8%) with structural anomalies. The prevalence per 10 000 births for singleton cases of normal karyotype was 1.6 (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. There was no significant trend in SIA, duodenal atresia or JIA prevalence over time (RR=1.0, 95% credible interval (CrI): 1.0 to 1.0, for each) but SIA and duodenal atresia prevalence varied significantly between participating registers (p=0.03 and p=0.04, respectively). There was no increased risk of SIA in mothers aged <20 years compared to mothers aged 20 to 29 (RR=1.3, 95% CrI: 1.0 to 1.8; p=0.08).

Conclusion This study found no evidence of a temporal trend in the prevalence of SIA, duodenal atresia or JIA although SIA and duodenal atresia rates varied between geographic areas.