This retrospective review looked at endothelial cell counts (ECC) following penetrating keratoplasties (PKP) performed in infants within the first year of their life. One hundred eyes of 71 patients had their first PKP during the study period (1998-2013). In 30% PKP had failed. Non-contact specular microscopy was available for analysis from 21 eyes with clear grafts. The most common indications for PKP was Peters anomaly (76.2%) with 11 patients with Peters type 1 and five patients with type 2, followed by posterior polymorphous corneal dystrophy (9.5%); congenital glaucoma (secondary to Axenfeld–Rieger syndrome) with corneal endothelial dysfunction (9.5%); and congenital hereditary endothelial dystrophy (4.5%). Ten eyes (47.6%) had additional intraocular surgeries after corneal transplantation after median time of 6.4 months. Overall ECC decreased by median of 59% between preop and last follow-up (mean of 49 months). The most marked decrease happened within the first two years after transplant with subsequent plateauing. All eyes with a follow-up of over 100 months had ECC higher than 800 cells per square millimetre; significantly better than the ECC reported in adults. Donor size of 6mm or smaller, older donor age, additional intraocular surgeries, and the presence of glaucoma did not adversely affect the final ECC. Statistically significant lower final ECC was noted in eyes that had iris adhesions to the graft-host junction versus eyes with no synechiae. This study is the first one to examine long-term ECC in paediatric population.