 Lung transplantation is indicated when end-stage lung diseases no longer respond to available standard therapy, making life expectancy short and associated with disability. Acute and chronic rejection are common complications following transplantation, indicating screening bronchoscopies and transbronchial biopsies at three month intervals the first two years, in addition to clinically indicated procedures when rejection or infection is suspected. Transbronchial biopsies carry associated risks bleeding, pneumothorax. Chronic rejection is characterized by progressive obliteration of distal airways Bronchiolitis Obliterans-BO-. BO requires open lung biopsy for diagnosis. Alternatively, a clinical surrogate Bronchiolitis Obliterans Syndrome, characterized by decline in Forced Expired Volume in 1 second not explained by acute rejection or infection is used for diagnosis. The new technique of confocal endo-microscopy enables sub-surface visualization of tissue in vivo during bronchoscopic procedures using a probe-based confocal microscope, integrated to a standard endoscope. Bronchiolar and alveolar structures can be visualized at a cellular and nuclear level, and these images can be saved and reviewed. This new technology could potentially identify acute and chronic rejection, thus offering and alternative to transbronchial biopsies. We expect to describe a new alternative to diagnose acute and chronic rejection using confocal microscopy images obtained endoscopically, obviating complications of transbronchial biopsies. 