Intratracheal delivery of stem cells into injured or diseased lungs can provide a variety of therapeutic and immunomodulatory effects for the treatment of acute lung injury and chronic lung disease. While the efficacy of this approach depends on delivering the proper cell dosage into the target region of the airway, tracking and analysis of the cells have been challenging, largely due to the limited understanding of cell transport and lack of suitable cell monitoring techniques. We report on the transport and deposition of intratracheally delivered stem cells as well as strategies to modulate the number of cells (e.g., dose), topographic distribution, and region-specific delivery in small (rodent) and large (porcine and human) lungs. We also developed minimally invasive imaging techniques for real-time monitoring of intratracheally delivered cells. We propose that this approach can facilitate the implementation of patient-specific cells and lead to enhanced clinical outcomes in the treatment of lung disease with cell-based therapies.