Malrotation of the intestines occurs as a result of failure of normal intestinal rotation and fixation during early pregnancy. This study examined the epidemiology of malrotation in Hawaii during 1986–99, using data from a population-based birth defects registry. There were 81 cases of malrotation, resulting in a rate of 2.86 per 10 000 live births and fetal deaths. The first-year mortality rate was 15.8%. Other major birth defects were reported for 93.8% of the cases. The malrotation rate during 1993–99 was significantly higher than the rate during 1986–92 (rate ratio [RR] 1.42, 95% confidence interval [CI] 1.04, 1.90). The malrotation rate was inversely proportional to maternal age (P = 0.028). Compared with whites, the malrotation rate was significantly higher among Far East Asians (RR 1.95, 95% CI 1.12, 3.17), Pacific Islanders (RR 2.41, 95% CI 1.63, 3.44) and Filipinos (RR 1.82, 95% CI 1.02, 3.01). Malrotation rates did not differ significantly by sex (RR 0.98, 95% CI 0.70, 1.34) or plurality (RR 1.86, 95% CI 0.38, 5.44) but were significantly higher among livebirths with birthweight < 3000 g (RR 3.90, 95% CI 2.83, 5.24). With no other population-based studies of malrotation found in the literature, this study adds to the knowledge of the epidemiology of malrotation.