Amelogenins, a family of extracellular matrix proteins of the dental enamel, are transiently but abundantly expressed by ameloblasts during tooth development. Amelogenins seem to regulate the formation of crystallites during the secretory stage of enamel development, while they are specifically degraded during tooth-bud maturation. In this paper we report the characterization of the AMGX and AMGY genes on the short arms of the human X and Y chromosomes which encode the amelogenins. Our studies on the expression of the amelogenin genes in male developing tooth buds showed that both the AMGX and AMGY genes are transcriptionally active and encode potentially functional proteins. We have isolated genomic and cDNA clones from both the AMGX and AMGY loci and have studied the sequence organization of these two genes. Reverse transcriptase (RT)PCR amplification of the 5' portion of the amelogenin transcripts revealed several alternatively spliced products. The splicing pattern observed in the Y-derived mRNA varies from that of the X-derived mRNA. The promoter regions from both genes and the predicted amelogenin protein sequences are presented. This information will be useful for studying the molecular basis of X-linked amelogenesis imperfecta, for understanding the evolution and regulation of gene expression on the mammalian sex chromosomes, and for investigating the role of amelogenin genes during tooth development.