Heparan sulphate 6- O -sulphotransferase (HS6ST) catalyses the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in HS. We previously described the occurrence of three isoforms of mouse HS6ST, mHS6ST-1, -2, and -3 [Habuchi, Tanaka, Habuchi, Yoshida, Suzuki, Ban and Kimata (2000) J. Biol. Chem. 275, 2859-2868]. In the present study, we have characterized HS6ST-2 and HS6ST-1 human isologues, including their chromosomal localizations. In the process of their cDNA cloning, we found two forms of HS6ST-2: the original (hHS6ST-2) and a short form (hHS6ST-2S) with 40 amino acids deleted. Both hHS6ST-2 and hHS6ST-2S catalysed the same sulphation reaction, but their preferences for sulphation sites in HS substrates were different. Dot-blot analysis of the two forms showed that the original form was exclusively expressed in adult and foetal brain tissues, whereas the short form was expressed preferentially in ovary, placenta and foetal kidney, suggesting that the expression of two forms of hHS6ST-2 is strictly regulated to yield tissue-dependent differences in the fine structure of HS. A refined analysis of their reaction products has led us to another finding, that HS6STs could also transfer sulphate to N -sulphoglucosamine residues located at the non-reducing terminal of HS with high affinity.