To detect conjunctival epithelial cells with donor derived genome following human haematopoietic stem cell transplantation. Conjunctival biopsies from allotransplanted females were stained for the Y-chromosome, cytokeratin, and CD45 followed by a DAPI counterstain and CD68 staining and were then evaluated by laser-scanning confocal microscopy and 3D analysis. In 5 patients donor derived epithelial cells identified as Y+/DAPI+/CK+/CD45-/CD68-/epithelial morphology could be found (57%) with a mean incidence of 5.4% (range 2.42% - 7.94%). Our study demonstrates that besides the already published results in liver, colon, lung, skin and oral mucosa, epithelial cells with donor-derived genome also emerge in the conjunctiva following human HSCT. The biological significance and the underlying mechanism of these findings need further clarification.