Congenital diseases of the liver and gastrointestinal tract in children areincreasingly compatible with survival into adulthood. Liver and intestinal transplantation have largely contributed to improved outcomes but come with their share of problems and co-morbidities affecting both longevity and quality of life. Therefore, in the long run, alternative therapies are warranted. Among the most popular prospects are cell-based therapies. The development of cellbased therapies requires in vitro manipulation and recapitulation of developmental cascades to ensure differentiation into the selected cell-type and avoid uncontrolled proliferation and malignant transformation. Therefore,understanding early development in vivo is necessary prior to directing cell fate in vitro. In the case of liver development, early signaling cascades are now well characterized and applicable to cells in vitro, albeit with limited success.Intestinal cell-based therapy is less advanced, although recent studies are promising in terms of healing epithelial disease. The study of gastrointestinal development, on the other hand, has identified a large number of genes important in development and linked to congenital diseases. This thesis reviews how understanding cell-fate decisions and development is of use both in apprehending and treating congenital diseases of the liver and gastrointestinal tract.