Thrombomodulin (TM) is an integral membrane glycoprotein, which occurs as both a chondroitin sulfate (CS) proteoglycan (PG) form (-TM) and a non-PG form without a CS chain (␣-TM) and hence is a part-time PG. An ␣-TM preparation isolated from human urine contained the glycosaminoglycan linkage region tetrasaccharide GlcUA1-3Gal1-3Gal1-4xylose, and the nonreducing terminal GlcUA residue is 3-Osulfated. Because the human natural killer-1 sulfotransferase (HNK-1ST) transfers a sulfate group from 3-phosphoadenosine 5-phosphosulfate to the C-3 position of the nonreducing terminal GlcUA residue in the HNK-1 antigen precursor trisaccharide, GlcUA1-3Gal1-4GlcNAc, the sulfotransferase activity toward the linkage region was investigated. In fact, the activity of HNK-1ST toward the linkage region was much higher than that toward the glucuronylneolactotetraosylceramide, the precursor of the HNK-1 epitope. HNK-1ST may be responsible for regulating the sorting of ␣-and -TM. Furthermore, HNK-1ST also transferred a sulfate group from 3-phosphoadenosine 5-phosphosulfate to the C-3 position of the nonreducing terminal GlcUA residue of a chondroitin chain. Intriguingly, the HNK-1 antibody recognized CS chains and the linkage region if they contained GlcUA(3-O-sulfate), suggesting that HNK-1ST not only synthesizes the HNK-1 epitope but may also be involved in the generation of part-time PGs.