Members of the trypsin-like and chymotrypsin-like kallikrein family are important in the desquamation process. In this study, we isolated cDNA clones encoding trypsinogen 4 (brain trypsinogen) and a previously unreported isoform of trypsinogen from a human keratinocyte cDNA library. The nucleotide sequence of the new isoform only differs from those of trypsinogen 3 (mesotrypsinogen) and trypsinogen 4 in an exon encoding the N-terminal region, indicating that this isoform is an alternative splicing variant of the mesotrypsinogen gene PRSS3. Both isoforms contained the sequence DDDDK-I, a putative cleavage site for activation by enteropeptidase. Thus, after activation, mesotrypsin would be produced. Immunohistochemical and in situ hybridization studies revealed that trypsinogens were expressed and localized in the upper epidermis, especially in the granular layer. In cultured keratinocytes, enteropeptidase mRNA was expressed at the confluent stage, and its expression was strongly upregulated after air exposure. Interestingly, it was synthesized and localized only at the granular layer, suggesting that the generation of active mesotrypsin is restricted to this layer. The enteropeptidase-cleavage product was also found at the same layer. When a skin equivalent model was cultured in the medium without air exposure, the cornified layer was not formed, and many cells expressed trypsinogens and enteropeptidase. Those cells were found to be TUNEL positive. Because mesotrypsin is resistant to naturally occurring trypsin inhibitors, confined expression of the isoforms of mesotrypsinogens and enteropeptidase may indicate that mesotrypsin is involved in keratinocyte terminal differentiation.