Unlike transplantation of other solid organs, vascularized mouse lung transplantation has only recently been developed. In this protocol, we describe a detailed method for performing a vascularized and aerated mouse orthotopic lung transplant, which to date represents the most physiological mouse model of lung transplantation. The procedure is divided into two separate portions consisting of donor harvest followed by implantation using the cuff technique for bronchovascular anastomoses. After a training period spanning several months, the procedure can be successfully mastered and, in experienced hands, requires similar to 90 min to perform. After an initial learning curve, perioperative survival is close to 100%. As the donor hematopoietic cells in the transplanted lung are replaced by those of the host over time, thereby creating a 'chimeric lung,' this model represents a novel research tool for the study of transplantation biology as well as other disease processes, such as malignancies.