Harlequin ichthyosis (HI) is a severe congenital ichthyosis in which newborn infants are covered with a thick plate of stratum corneum. We examined skin specimens from a variety of regions of the body including the scalp, face, tongue, trunk, upper and lower extremities, digits, palms, and soles of three fetuses affected with HI that were diagnosed prenatally. In all the skin regions, characteristic morphological abnormalities (absent or abnormal lamellar granules and intercellular lamellae, lipid inclusions in the cornified cells) were expressed in the late second trimester of the fetal period. The cornified cells in hair canals showed morphological abnormalities of HI more strongly than the interfollicular epidermis. Immunoblot study of epidermal extracts revealed that profilaggrin was much more prominent than filaggrin in all the hairy skin regions where the hair canals were extensively keratinized, but filaggrin was prominent in the palm. These observations support the idea that, in the hairy skin, HI phenotype expression is associated with keratinization and abnormal filaggrin metabolism in hair. In addition, the prenatal diagnosis or prenatal exclusion of HI is thought to be possible from whichever site of the fetal body the skin biopsy is taken in the late second trimester of the fetal period.