Purpose To compare anti-human cornea and anti-bovine cornea serum reactivity in corneal transplantation and pathology. Methods We investigated the presence of IgG and IgM antibodies to bovine corneal extract (BCE) and human corneal extract (HCE) by ELISA in 48 healthy adults and in 30 corneal allograft recipients before and after grafting. Baseline levels of antibodies in healthy controls served to establish a positivity threshold. Anti-HLA antibodies were investigated in all patients. Results Preoperatively, five and one patient were positive respectively for IgG and IgM anti-BCE; one and ten patients were positive for IgG and IgM anti-HCE. The presence or absence of antibodies was not modified after grafting, and was not associated with rejection. Anti-HCE of the IgM class were more frequent in patients with keratoconus. Two patients had anti-HLA antibodies. Conclusions Antibodies to non-HLA corneal antigens are detectable in corneal allograft recipients. Reactions against bovine and human substrates differ in frequency and class. This reactivity is not modified after grafting or rejection, but is increased in corneal disorders, including keratoconus.