Various kinds of biomaterials that have biocompatibility and biodegradability have been used for the tissue engineered organ reconstruction. Their characteristics have relationship with functional and morphological reconstruction. However, it is not clear which types of biomaterials provide the best outcomes after transplantation. For the reason, in this study, to compare synthetic biomaterial and natural biomaterial, we developed two kinds of patches to compare affects of biomaterials for cell transplantation and organ reconstruction. The one was coated with PLGA sheet and the other was coated with autologous dermal sheet. Cultured PKH26-labeled cells were seeded on the patches and then the patches were transplanted onto tracheas. After three months, we found that each biomaterial had a different tracheal reconstruction pattern: the PLGA patch was suited for airway patency(tracheal passage with stable inside diameter for air exchange) but not for epithelial layer reconstruction whereas the dermal patch was suited for epithelial layer reconstruction but not for airway patency. Consequently, while selecting biomaterials for transplantation and reconstruction, not only their biological effects on the body but also their effects on organ morphology and function should be considered.