Gastrointestinal atresia is a major cause of bowel obstruction in the newborn. Experimental models and clinical observations have demonstrated the heterogeneous nature of its pathogenesis. A proportion is due to late intra-uterine vascular insults and some are genetic in nature. Epidemiological studies have found gastrointestinal atresia to occur with other birth defects, in particular VACTERL anomalies, suggesting that a subset of cases may result from an early disturbance to intestinal morphogenesis. Adriamycin is teratogenic in rats, producing gastrointestinal atresia and VACTERL anomalies. The mouse is the foremost mammal studied by developmental biologists, offering an expanding wealth of knowledge and scientific research techniques. The aim of this study was to create an Adriamycin mouse model for investigating the development of gastrointestinal atresia. CBA/Ca mice were accurately time-mated (n = 30). Four different doses of Adriamycin (0-saline control, 4, 5 and 6 mg/kg) at three different timings of injections were compared (12 groups). Dams received two intraperitoneal injections, 24 h apart, commencing on day 7, 7.5 or 8. Foetuses were harvested on day 18. Gastrointestinal atresia and VACTERL anomalies were examined using a dissecting microscope. Adriamycin produced type IIIa gastrointestinal atresia in six treatment groups. The effect of Adriamycin depended on the timing and dose of the injections. VACTERL anomalies were only found in four treatment groups, proposing overlapping critical embryological windows for these malformations. Gastrointestinal atresia can be induced by the teratogen Adriamycin, occurring with and without VACTERL anomalies. This produces a reproducible mouse model in which the molecular pathogenesis of gastrointestinal atresia may be studied.