Aim: To investigate the site of alloantigen presentation in the rat following orthotopic corneal transplantation. Methods: Adult inbred Fischer 344 rats received penetrating corneal allografts from inbred Wistar Furth donors (n=17), without lymphadenectomy. A second group (n=8) underwent bilateral removal of superficial cervical and facial lymph nodes 7 days before transplantation. A third group (n=9) underwent bilateral removal of superficial cervical, facial, internal jugular and posterior cervical nodes. Graft survival was assessed by corneal clarity and rejection was confirmed histologically. Results: All allografts underwent rejection. The median time to rejection for unmodified allografts was day 15, compared with day 14.5 for minimally lymphadenectomised recipients and day 18 for more extensively lymphadenectomised recipients (p>0.05, all comparisons). The median day to rejection for the combined group of lymphadenectomised rats was day 17 (p>0.05 compared with unmodified grafts). The rejection process was similar in all recipients. Conclusions: Removal of multiple lymph nodes in the neck and thorax did not significantly influence the incidence, tempo or nature of the corneal allograft response. Sensitisation and clonal expansion of corneal alloantigen-reactive cells cannot occur only in superficial cervical, facial, internal jugular and posterior cervical lymph nodes in the rat.