Purpose The purpose of this study was to assess the endothelium of corneal grafts by in vivo confocal microscopy (IVCM), and to evaluate an automated endothelial software system in comparison with a manual cell count and planimetry. Patients and methods Overall, 40 corneal grafts (20 deep anterior lamellar keratoplasties (DALKs) and 20 penetrating keratoplasties (PKs)) were assessed by scanning-slit IVCM. The endothelial cell density (ECD) was estimated with the automated and the manual cell count method of the instrument's Nidek Advanced Vision Information System (NAVIS) software. The results were compared with planimetry as the reference method, and the agreement was assessed. Results The mean ( ± SD) automated ECD was 2278 ± 524 cells/mm 2 (range 1167-3192 cells/mm 2 ), whereas the manual cell count method gave significantly lower ECDs with a mean of 1213±677 cells/mm 2 (range 218-2440 cells/mm 2 ; Po0.001). The manual cell counts were also significantly lower than those by planimetry, with a mean ECD of 1617 ± 813 cells/mm 2 (range 336-2941, Po0.001). Bland-Altman analyses indicated that the limits of agreement (LoA) between the automated and the planimetry method were À671 and þ 1992 cells/mm 2 , whereas they were À1000 and þ 202 cells/mm 2 when comparing the manual cell counts with planimetry. Conclusion Following keratoplasty, the NAVIS automated method is likely to overestimate endothelial cell counts due to oversegmenting of the cell domains. Automated ECDs are substantially higher than those by the manual counting method or planimetry. The differences are considerably larger post-keratoplasty than for normal corneas, and the methods should not be used interchangeably.