To date, five distinct alpha chains have been identified in basement membrane collagen IV. We have cloned a gene encoding a new alpha chain belonging to basement membrane collagen IV by cDNA isolation under low stringency conditions. Isolation of overlapping clones and the technique of 5' rapid amplification of cDNA ends enabled us to derive the primary structure of the entire polypeptide. The deduced collagen polypeptide contained 1678 amino acid residues, including a 21-residue signal peptide, a 24-residue amino-terminal NC domain, a central 1405-residue collagenous (COL1) domain, and a 228-residue carboxyl-terminal NC1 domain. We have designated this newly found alpha chain as the alpha 6(IV) chain. The gene was mapped to chromosome Xq22 by in situ hybridization of metaphase lymphocytes. This is the same region of chromosome X where the gene coding for the alpha 5(IV) collagen chain (COL4A5) resides. Mutations in COL4A5 have been characterized in more than 50 patients with Alport syndrome. However, some of the X-linked cases of Alport syndrome are not apparently caused by COL4A5 mutations. The gene we describe in this paper therefore seems to be a candidate for mutations in this group of Alport syndrome patients.