Atresia and stenosis are some of the most common birth defects affecting the small intestine. Few population-based studies have examined the epidemiology of small intestinal atresia/stenosis. Eighty-two cases of small intestinal atresia/stenosis were identified through a population-based birth defects registry in Hawaii during 1986-2000. The relationships of various clinical and demographic factors with small intestinal atresia/stenosis and duodenal atresia/stenosis were examined. The small intestinal atresia/stenosis and duodenal atresia/stenosis rates were 2.9 per 10,000 live births [95% confidence interval (CI) 2.3-3.6] and 1.3 per 10,000 live births (95% CI 1.0-1.9), respectively. No secular trend was observed (P = 0.067 and 0.090, respectively). Maternal age risk for small intestinal atresia/stenosis was U-shaped, while duodenal atresia/stenosis rates were highest with maternal age of 35 years or more. Small intestinal atresia/stenosis was substantially more common among Far East Asians than Caucasians [rate ratio (RR) 1.96, 95% CI 1.24-2.94]. Duodenal atresia/stenosis risk was higher in Hawaii County than in Honolulu County (RR 2.55, 95% CI 1.10-5.02). Small intestinal atresia/stenosis was also associated with low birth weight (RR 11.50, 95% CI 8.05-15.92), low gestational age (RR 8.60, 95% CI 6.34-11.41) and multiple births (RR 3.79, 95% CI 1.39-8.24). In conclusion, this study found associations between small intestinal atresia/stenosis and maternal age, maternal race/ethnicity, county of residence, birth weight, gestational age and plurality, but not delivery period. Many of the associations between small intestinal atresia/stenosis and other factors noted in this investigation were similar to those reported by other studies.