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The aim of this study was to describe the prevalence of esophageal atresia/stenosis and small intestinal atresia/stenosis in Nagano, Japan, together with associated anomalies, prenatal diagnosis and survival.A population-based cohort study of the prevalence of esophageal atresia/stenosis and small intestinal atresia/stenosis was conducted in Nagano in January 1993–December 2011. The Mann–Whitney test, χ2 test and Kruskal–Wallis test were used to compare variables. P < 0.05 was considered statistically significant.In total, 74 cases of esophageal atresia/stenosis and 87 cases of small intestinal atresia/stenosis (31 duodenal, 56 jejuno-ileal) were identified. Prevalences were 1.97 for esophageal atresia/stenosis and 2.23 for small intestinal atresia/stenosis (0.83 for duodenal atresia/stenosis and 1.49 for jejuno-ileal atresia/stenosis) per 10 000 births, respectively. The prevalence of esophageal atresia/stenosis increased significantly from 1993–2001 to 2002–2011 (relative risk [RR], 1.6), as did the prevalences of duodenal atresia/stenosis (RR, 2.2) and jejuno-ileal atresia/stenosis (RR, 3.1). Chromosomal anomalies, particularly trisomy 21, were seen significantly more often in association with duodenal atresia/stenosis (55%) than with esophageal atresia/stenosis (28%, P < 0.01) or jejuno-ileal atresia/stenosis (2%, P < 0.01). The proportion of patients associated with prenatally diagnosed chromosomal anomaly was higher compared to postnatal diagnosis (P < 0.01) in the esophageal atresia/stenosis group.The prevalence of esophageal and small intestinal atresia/stenosis increased significantly from 1993–2001 to 2002–2011. Prenatally diagnosed esophageal atresia/stenosis is associated with multiple anomalies, particularly chromosomal anomalies, compared to other small intestine atresia/stenosis.