Corneal epithelial cells synthesize an acidic (55 kDa) K12 and a basic (64 kDa) K3 keratin as their major differentiation products during an advanced stage of differentiation. In this paper, we describe the cDNA cloning of rabbit K12 keratin. We used a 36 base pairs (bp) oligonucleotide corresponding to a consensus sequence of many known acidic keratins as a probe to screen a cDNA library of normal rabbit corneal epithelium. Several partial cDNA clones were isolated. Hybrid-selection showed that the 3′keratin chain-specific portion of the cDNA hybridizes with K12 mRNA. A rabbit antiserum raised against the C-terminus of the cDNA-deduced amino acid sequence recognizes, in immunoblotting, the K12 keratin. In situ hybridization showed that K12 mRNA is present in all cell layers of central corneal epithelium, but in only the suprabasal cells of limbal epithelium indicating a parallel expression pattern between K12 and K3. Cultured rabbit corneal epithelial cells initially synthesize K14/K5 keratins, but later when the cells become heavily stratified they synthesize large quantities of K12 and K3 mRNAs, as detected by Northern blotting. Cultured esophageal epithelial cells do not make K12 mRNA confirming the tissue-specificity of K12 expression. Although it has been suggested that conjunctival epithelial cells can trans-differentiate into a bona fide corneal epithelium, we showed here that cultured conjunctival cells do not synthesize significant amounts of K12/K3 mRNAs. These results strongly suggest that conjunctival epithelial cells, whose differentiation can be modulated significantly by the extracellular matrix, form a lineage intrinsically distinct from the corneal/limbal epithelial lineage.