To identify the anagen hair follicle-specific proteins, we screened the cDNA library prepared from the murine skins of anagen phase by the differential hybridization technique. Fifty-four cDNA clones expressed specifically in anagen phase were isolated, and most were found to correspond to known proteins in the hair follicles. Alternatively, we isolated a cDNA clone encoding a novel protein that possessed an entire open reading frame of 501 base pairs. This protein with a molecular weight of 17.9 kDa has no specific motifs nor significant homology to proteins already reported, although it contains some direct repeats that are often observed in intermediate filament-associated proteins and has a similar amino acid composition as a member of them. Northern blot analysis demonstrates that the transcript of this protein is skin specific, and that it is present in mid- and late anagen but not in catagen, telogen, and early anagen phases. The transcript appears to be expressed specifically in the keratogenous zone of the cortical cells of hair follicles, as exhibited by in situ hybridization. Furthermore, immunohistochemical study confirms that the protein is distributed in the cytoplasms of the keratinizing cortical cells and is undetected in the completely keratinized ones. These results suggest that this protein can be identified as a new member of intermediate filament-associated proteins and is related to the keratinization of the cortical cell layer in mouse hair. Therefore, we have termed this novel protein mKAP13 according to the unified nomenclature.