Lamellar (component cell) corneal transplantation is replacing penetrating keratoplasty for some corneal disorders in humans, but the relative risks of immunological graft rejection for the two procedures remain uncertain. A model of component endothelial cell keratoplasty (endokeratoplasty) was developed in outbred sheep. Clinical and histological graft outcomes after endokeratoplasty were then compared with contemporaneous penetrating corneal allografts. No topical or systemic immunosuppression was administered to any recipient sheep. Endothelial cell allografts (n = 10) took significantly longer to achieve perfect transparency following surgery than did penetrating corneal grafts (n = 7) (day 10 vs. day 4; p = 0.003; two-tailed Mann-Whitney U test). The median day to rejection of penetrating grafts was postoperative day 18; for endothelial cell grafts, it was day 48 (p = 0.04; two-tailed Mann-Whitney U test). The clinical courses of the two procedures were therefore quite different. Penetrating grafts gained clarity quickly but exhibited rapid graft neovascularization. Clinical rejection was preceded by inflammation in the anterior segment. Endothelial cell grafts exhibited a fluctuating, more indolent course of opacification, although all did eventually fail. Histological analysis confirmed immunological rejection in all failed grafts, but with different patterns of leukocytic infiltration in endokeratoplasties compared with penetrating keratoplasties. Inflammatory cells in endothelial cell grafts were generally fewer in number and were more often found in the posterior stroma. We conclude that, in the absence of immunosuppression, all endothelial cell allografts do undergo immunological rejection, albeit at a slower rate than penetrating grafts.