As part of a program designed to characterize human hair keratin genes and their expression, we present the cDNA sequences and deduced amino acid sequences of three type-II hair keratins hHb3, hHb5, and hHb6, which by virtue of their amino acid homologies are the orthologs of the previously described sheep wool keratins, K2.10, K2.12, and K.211 [29]. Amino acid sequences comparisons of these keratins, including the previously characterized human K2.9 ortholog hHb1, show extreme conservation not only in the alpha-helices but also in the aminoterminal and proximal carboxyterminal domains. They also demonstrate higher sequence relationships between hHb1, hHb3, and hHb6 as compared to hHb5, which exhibits chain-specific sequences in both the head and tail domains. In situ hybridization studies using specific 3'-probes for the four type-II hair keratins reveal sequential patterns of gene expression in human anagen follicles. Remarkably the onset of hHb5 mRNA synthesis occurs immediately above a small population of matrix cells at the base of the hair bulb and the trichocytes lining the dermal papilla. hHb5 mRNA synthesis extends upward through the matrix and ends in the lower part of the cortex of the hair shaft. In contrast, both hHb1 and hHb3 mRNA synthesis begins simultaneously in the cortex 10-15 cell layers above the apex of the dermal papilla, thus partially overlapping that of hHb5 but continuing to a point well beyond hHb5 in the upper cortex. Synthesis of hHb6 mRNA starts slightly higher than either hHb1 or hHb3 mRNA and proceeds much farther up into the keratogenous zone of the hair shaft. Our study demonstrates that the differentiation of human hair in terms of hair keratin expression begins much earlier than previously assumed, i.e. in lower matrix cells of the hair bulb. This early phase of hair differentiation is followed by a late cortical phase of terminal differentiation which comprises at least three type-II hair keratins in the zone of elongation and the keratogenous zone of the hair shaft.