We were recently successful in performing the first human tissue engineered tracheal transplantations using biologic or artificial scaffolds, the patient’s own bone marrow derived stem cells, and bioactive molecules. We will present the lessons learned from our bench-to-bedside research including long-term clinical results, interactions between cells and neighboring tissues, circulating stem/progenitor cells, and mathematical models for understanding and predicting regeneration. We will also discuss our initial results for other intrathoracic organ (esophagus, diaphragm, heart and/or lung) regeneration. Cell therapy will be discussed in regards to our clinical studies for failing lungs.