A family of five 1,3-galactosyltransferases has been characterized that catalyze the formation of Gal1, 3GlcNAc and Gal1,3GalNAc linkages present in glycoproteins and glycolipids (3GalT1, -2, -3, -4, and -5). We now report a new member of the family (3GalT6), involved in glycosaminoglycan biosynthesis. The human and mouse genes were located on chromosomes 1p36.3 and 4E2, respectively, and homologs are found in Drosophila melanogaster and Caenorhabditis elegans. Unlike other members of the family, 3GalT6 showed a broad mRNA expression pattern by Northern blot analysis. Although a high degree of homology across several subdomains exists among other members of the 3-galactosyltransferase family, recombinant enzyme did not utilize glucosamine-or galactosamine-containing acceptors. Instead, the enzyme transferred galactose from UDP-galactose to acceptors containing a terminal -linked galactose residue. This product, Gal1,3Gal is found in the linkage region of heparan sulfate and chondroitin sulfate (GlcA1,3Gal1,3Gal1,4Xyl-O-Ser), indicating that 3GalT6 is the so-called galactosyltransferase II involved in glycosaminoglycan biosynthesis. Its identity was confirmed in vivo by siRNA-mediated inhibition of glycosaminoglycan synthesis in HeLa S3 cells.