The zeta-subunit is the most recently characterized stoichiometric human TCR component. In this study we describe the molecular organization of the human zeta-gene. The zeta transcript is generated as the spliced product of eight exons that are separated by distances of 0.7 kb to more than 8 kb. Ribonuclease protection studies revealed multiple transcription initiation sites distributed over a range of approximately 115 bases. A variable number tandem repeat restriction fragment polymorphism contained within the structural gene has allowed for the localization of zeta within the human genome. Additionally, a restriction fragment polymorphism within the Fc gamma RII-Fc gamma RIII gene cluster has allowed for its localization on the map of human chromosome 1q and for the establishment of its linkage to the zeta-gene locus. A region that is highly homologous on a nucleotide level with the eta-exon of the murine zeta-gene is localized to the 3' region of the human zeta-gene. Surprisingly, translation of this region into protein results in a structure that is markedly divergent from its murine counterpart. This finding has important implications regarding the potential role of eta in T cell function.