OBJECTIVE To determine the short-term fate of the host endothelium and Descemet membrane after non-Descemet stripping automated endothelial keratoplasty (nDSAEK). METHODS Eight unilateral DSAEK (n = 4) or nDSAEK (n = 4) surgeries were performed in the right eyes of 8 rabbits. Corneal transparency and thickness were followed-up by slit-lamp microscopy, and 2 weeks postoperatively, corneas were evaluated by immunohistochemistry and transmission electron microscopy. RESULTS Corneas remained clear after both DSAEK and nDSAEK. One week after DSAEK, the stroma-to-stroma surgical interface was identifiable as a zone of fibrotic tissue a few microns thick, whereas in the nDSAEK group, the recipient corneal endothelium and Descemet membrane were clearly visible at the graft-host interface. The retained endothelial cells were positive for Na/K-ATPase but assumed a markedly different morphology from healthy endothelial cells, with cell processes extending into the graft stroma or engulfing strands of irregularly dissected grafted stromal tissue where they occasionally appeared to compartmentalize the transplanted matrix and became detached from the underlying Descemet membrane. CONCLUSIONS Host endothelial cells 2 weeks after nDSAEK express markers of pump function, but appear to be morphologically altered, occasionally detaching from the adjacent Descemet membrane, extending into the graft stroma or engulfing strands of the grafted stroma at the interface. The short-term persistence and subsequent phenotypical alternation of residual endothelial cells, aligned to structural changes to Descemet membrane, might influence graft adherence after nDSAEK.