N-Heparan-sulfate sulfotransferase catalyzes the transfer of sulfate from 3'-phosphoadenilyl sulfate to the nitrogen of glucosamine in heparan sulfate. This reaction is an obligatory step for subsequent epimerization of D-glucuronic to L-iduronic acid and of O-sulfation of the sugar chains. We have purified this sulfotransferase from rat liver membranes to apparent homogeneity using a combination of conventional and affinity chromatography on DEAE-Sephacel, heparin-agarose, 3',5'-ADP-agarose, wheat germ-Sepharose, and finally a glycerol gradient. The pure enzyme is a glycoprotein with an apparent molecular weight of 97,000. It was enriched in specific activity 65,000-fold over the homogenate. The recovery of activity was 4% of that of the homogenate. Preliminary enzymatic characterization of the purified sulfotransferase indicates a high degree of substrate specificity. Transfer of sulfate occurs to heparan sulfate, N-heparan sulfate, and N-desulfated heparin, but not to N-acetylated heparan sulfate, N-acetylated heparin, chondroitin, chondroitin sulfate, and tyrosine-containing tripeptides.