Peptidylarginine deiminases (PAD) catalyze the conversion of arginine residues to citrullines. Five isoforms are known that present distinct tissue locations. In the epidermis, like in the skin, only PAD1, 2, and 3 are expressed. Their pattern of expression in skin appendages is not known. Here, confocal microscopy analysis using highly specific antibodies demonstrated that PAD1 and 3 are expressed in human anagen hair follicles, PAD1 and 2, in arrector pili muscles and sweat glands, whereas no PAD were detected in sebaceous glands. PAD1 was detected in the cuticle and the Huxley layer of the inner root sheath (IRS), and in the companion layer. PAD3 was localized in the medulla, and in the three layers of the IRS. Using anti-modified citrulline antibodies, we also showed that deiminated proteins appeared in the lower part of the IRS, first in the Henle layer, then in the cuticle, and finally in the Huxley layer. Our data demonstrate that PAD3 is the enzyme that deiminates trichohyalin in the medulla and the Henle layer, indicate that PAD1 and 3 are involved in the hair follicle program of differentiation, and suggest a role for PAD1 and 2 in the physiology of sweat glands and arrector pili muscles.