Implantable devices comprising a scaffold, cells, and/or therapeutic molecules are provided. Uses include inhibition of pathological immunity, elaboration of therapeutic growth factors, and immune augmentation. The implantable device may contain a porous substrate structure to which therapeutic cells are adherent, which can be implanted and explanted from a patient. In another embodiment, a medical device includes a porous substrate seeded with therapeutic cells, said device comprising of an additional layer allowing free exchange of molecules without cell escape. Said medical device is seeded with thymic medullary epithelial cells or progenitors of said thymic medullary epithelial cells. In conditions where tolerance to alloreactive donor cells is desired, the thymic medullary epithelial cells or progenitors thereof are derived from recipient cells. In conditions where tolerance to alloreactive recipient cells is desired, the thymic medullary epithelial cells or progenitors thereof are derived from donor cells.