To demonstrate in vivo confocal microscopic features of corneal allograft rejection that may be useful for differentiating graft rejection from other conditions. Corneal donor buttons from Dutch Belted (DB) pigmented rabbits were transplanted orthotopically into New Zealand White (NZW) recipient corneal beds. Slit-lamp and confocal microscopic examinations were performed every 3 days thereafter until the time of graft failure. Allograft-rejection signs began to appear during the fourth postoperative week. In epithelial rejection, small inflammatory cells were visualized forming a linear rejection line mixed with larger damaged epithelial cells. Subepithelial infiltrates (SEIs) could be discerned as aggregates of small and highly refractile inflammatory cells within the extracellular matrix. An area of stromal rejection showed increased reflectivity of stromal edema with numerous small infiltrated inflammatory cells. Keratic precipitate (KP) was visualized to be protruding into the anterior chamber with surrounding normal polygonal endothelial cells at its base. Endothelial rejection lines were formed by cellular aggregates of small inflammatory cells and damaged larger endothelial cells with pyknotic highly reflective nuclei. With the progression of endothelial rejection, damaged endothelial cells decreased in number, increased in size, and extended pseudopod-like cytoplasmic structures. In vivo confocal microscopy can provide us with detailed histopathology of corneal graft rejection, which might be useful for differentiating immune rejection from other graft conditions and may provide a technique for early diagnosis of rejection before slit-lamp findings.