We used a rabbit model to evaluate the interface embedded between the recipient corneas and transplanted donor corneal discs after non-Descemet's stripping automated endothelial keratoplasty (nDSAEK). Unilateral DSAEK and nDSAEK surgeries were performed on New Zealand white rabbits. In vivo confocal microscopy was performed to show: the changes in corneal endothelial cells embedded between the recipient corneas and the transplanted donor corneal discs (CEEB); and the interface opacity by z profile. Immunohistochemistry were performed to evaluate the functional change of CEEB at post-nDSAEK 3 months. Transmission electron microscopy was performed to evaluate the morphology of CEEB after nDSAEK at post-nDSAEK 1, 3, and 6 months. In vivo confocal microscopy showed a time-dependent decrease in the density of CEEB at postoperative 1, 2, or 3 months (P < 0.01). Interface opacity was higher in the nDSAEK group than the DSAEK group at all examination points, but the difference was statistically insignificant. At 3 months after surgery, the CEEB were negative for Na(+)/K(+)-ATPase staining. Staining with TUNEL showed apoptotic changes in some areas. During a 6-month observation, the CEEB showed a time-dependent thickening and loss of uniform thickness of cellular morphology. At 3 and 6 months post nDSAEK, extensions of the cellular processes into the donor graft stroma combined with intracellular vacuoles containing collagen-like materials were also found. After non-Descemet's stripping automated endothelial keratoplasty, the CEEB showed decreased density, loss of pump function, apoptosis and changed morphology. However, the interface opacity was not significantly greater compared with DSAEK eyes.