We investigated the immunohistochemical characteristics of corneal specimens in congenital aniridia and pemphigoid using various corneal markers to determine the status of the corneal epithelium. Conjunctivalization was clinically suspected in all corneas. Ten aniridia and seven pemphigoid paraffin-embedded corneal specimens were stained with periodic Schiff reagent (PAS) and antibodies against CK3/12, CK12, CK19, breast cancer resistance protein 1 (BCRP) and p63. Aniridia: six cases contained goblet cells, four were negative. Both groups had cases with (three of six; one of four) and without CK19 positivity and cases with (two of six; three of four) and without p63 positivity. All aniridia cases except two in the goblet cell group were CK3/12- and CK12-positive and BCRP-negative. Pemphigoid: only one of the seven cases contained goblet cells. This case stained positively for CK19, 3/12, 12 and p63 and negatively for BCRP. The other six cases were positive for CK3/12, five of which were positive for CK12; only one case was CK19-positive. Three cases were p63-positive and two BCRP-positive. The CK12 staining was heterogenous in most cases and was often found in the superficial layer. Three different stages of epithelial characteristics were found in congenital aniridia and pemphigoid: (i) CK19-negative and inhomogenous CK12-positive cases indicating epithelium mainly from (partly) CK12-deficient limbal stem cells; (ii) CK19- and/or goblet cell-positive and CK12-positive cases with their epithelia originating from CK12-deficient limbal stem cells and from incursing conjunctival cells; and (iii) CK19-positive and CK12-negative cases consisting of conjunctival cells alone.