The human mucosal lymphocyte-1 (HML-1) antigen is expressed on a subclass of T-lymphocytes known as intra-epithelial lymphocytes which are located between mucosal epithelial cells. The HML-1 complex is known to mediate adhesion of intra-epithelial T-lymphocytes to epithelial cell monolayers in vitro. We and others have shown that the HML-1 antigen is an integrin composed of the beta 7 subunit in association with a novel alpha subunit, alpha E. Here we report the cloning of the alpha E cDNA and its primary amino acid sequence. alpha E contained an inserted or I domain and was more homologous to the other I domain containing integrins than to the cleaved group of integrin alpha subunits. However, alpha E contained a unique extra domain of 55 amino acids located just NH2-terminal to the I domain without counterpart in other integrins. This extra domain contained a stretch of 18 consecutive charged residues and included a proteolytic cleavage site. Thus alpha E is the only I domain containing integrin alpha subunit that is also cleaved, and the cleavage site is distinct from that of members of the cleaved group of integrin alpha subunits. These structural features mark alpha E as an unusual member of the integrin family. High levels of alpha E and beta 7 mRNA were restricted to mucosal lymphocytes supporting the hypothesis that alpha E beta 7 plays a role in the localization or site-specific functions of intra-epithelial T-lymphocytes.