Post-translational conversion of arginine to citrulline residues is catalyzed by peptidylarginine deiminases (PAD). Although the existence of five isoforms of PAD has been reported in rodents and humans, their tissue distribution, substrate specificity, and physiological function have yet to be explored. In the epidermis, deimination of filaggrin and keratins is involved in maintaining hydration of the stratum corneum (SC), and hence the cutaneous barrier function. Here, RT-PCR, western blotting, and confocal microscopy analyses with anti-peptide antibodies highly specific for each of the PAD1-4 demonstrated that only PAD1-3 are expressed in mouse and human epidermis. PAD1 was detected in all layers, including the SC, and PAD2 in all the living layers, whereas PAD3 expression was shown to be restricted to the granular layer and lower SC. Moreover, PAD1 and 3 were observed to co-localize with (pro)filaggrin, and PAD2 to be located at the keratinocyte periphery in the stratum granulosum. We also detected PAD1 in extracts of superficial SC, where K1 is deiminated. Moreover, we showed that PAD1 and 3 are able to modify filaggrin in vitro. These data strongly suggest that each enzyme exerts a specific role in the course of epidermis differentiation.