To determine central keratocyte and subbasal nerve densities after penetrating keratoplasty (PK) in clear grafts and in grafts with late endothelial failure (LEF). Ninety-nine clear grafts of 74 patients and 21 grafts with LEF in 19 patients were examined by confocal microscopy at 1 to 31 years after PK. Keratocyte density and number of keratocytes in a full-thickness column of stroma with frontal area of 1 mm(2) were determined from images. Subbasal nerve fiber bundle density was measured in the central cornea as the visible length of nerve per frame area. Comparisons were made to normal corneas. Full-thickness keratocyte density in clear grafts (22,101 +/- 3,799 cells/mm(3), mean +/- SD, n = 99) was lower than in normal corneas (26,610 +/- 3,683 cells/mm(3), n = 63, P < .001) but did not differ from grafts with LEF (21,268 +/- 3,298 cells/mm(3), n = 12, P = .47). The number of keratocytes in clear grafts (10,325 +/- 1,708 cells, n = 99) was lower than in normal corneas (11,466 +/- 1,503 cells, n = 63, P < .001) but did not differ from grafts with LEF (10,778 +/- 1,760 cells, n=12, P = .39). Median subbasal nerve density in clear grafts (150 microm/mm(2), n = 94) was lower than in normal corneas (7,025 microm/mm(2), n = 76, P < .001), and nerve recovery correlated with time after PK (r = 0.36, P < .001, n = 94). Keratocyte density and number of keratocytes are decreased in penetrating grafts compared to normal corneas, but not compared to grafts with LEF. Subbasal nerve density does not recover to normal through 30 years after PK.