Some congenital skin disorders lacking structure proteins in the basement membrane zone carry severe prognosis because of severe erosion and skin dysfunction on the whole body. So far, several therapeutic strategies have been emerging for such disorders: 1. gene therapies, 2. protein therapies and 3. cell therapies. Cell therapies have a potential to affect skin systemically, and stem cell transplantation is one of the most hopeful candidates for treating severe congenital skin disorders such as epidermolysis bullosa, from a perspective of transdifferentiation and re-programming of stem cells. We review here the recent strategies and progress of stem cell transplantation for epidermolysis bullosa.