OBJECTIVE This study was designed to observe any changes to the corneal epithelium after penetrating keratoplasty. METHODS The corneal epithelia of 26 patients were observed by specular microscopy 1 week, 1 month, 3 months, and 6 months following penetrating keratoplasty. RESULTS After re-epithelialisation was confirmed by biomicroscopy 1 week after surgery, specular microscopy revealed many abnormal cells, including spindle shaped cells, nucleated cells, large cells, as well as irregular cell configurations. Although these abnormal findings tended to decrease with time, they were still present in some cases as much as 6 months postoperatively. Computerised morphometric analysis yielded mean cell areas of 1121 (SD 168) microns 2, 1139 (675) microns 2, 1712 (496) microns 2, and 1400 (377) microns 2 at 1 week, 1 month, 3 months, and 6 months respectively, all significantly greater than that of age matched controls (710 (151) microns 2). The shape factor decreased with time, but was still greater than the control level at 6 months. CONCLUSIONS This study demonstrates that epithelial abnormalities persist longer than expected after penetrating keratoplasty, and that these subtle changes can be detected by specular microscopic observation, potentially allowing for modification and enhancement of the wound healing process.