Regenerative medicine is the important field of science destined to solve problems of donororgans insufficiency and lifelong immunosuppression. We implement several projects devoted tonew approaches in tissue engineering and cell therapy for regeneration of intrathoracic organs, search for the optimal methods and transfer obtained results into clinic. Tracheal study was translated from bench to bedside: 4 transplantations were carried out with the use of nanocomposite scaffolds, seeded with patient’s bone marrow cells. For the diaphragm, lungs, heart and oesophagus biological scaffolds we worked out modified detergent-based agitation or perfusion decellularization methods in special bioreactors. Recellularization was performed usingmultipotent mesenchymal stromal cells. Obtained scaffolds were characterized by morphological, immunohistochemical and spectrophotometry methods, PCR, flow cytofluorometry, cell viability and biomechanical testing, electronic microscopy. DNA content and extracellular proteins were quantitatively and qualitatively measured. Successful rat orthotopic transplantations were performed with diaphragm and oesophagus scaffolds.