Heparan sulfate O-sulfotransferases catalyze the O-sulfation of the glucosamine and uronic acid residues of heparan sulfate, thereby determining the binding sites for ligands necessary for important biological functions such as the formation of morphogen gradients and growth factor signaling. Here we investigated the localization of the three heparan sulfate 6-O-sulfotransferase (HS6ST) isoforms and the mechanism of their localization. All three GFP-tagged HS6STs localized in the Golgi apparatus. C-5 epimerase and HS2ST have been shown to form complexes that facilitate their localization in the Golgi but we found that the absence of HS2ST did not alter the localization of any of the HS6STs. Neither the forced expression of HS2ST in the rough endoplasmic reticulum (ER), the deletion of most of the lumenal domain nor increasing the length of the transmembrane domain had any effect on the localization of HS6STs. However, deletions in the stem region did affect the Golgi localization of the HS6STs and also reduced their sulfotransferase activity and oligomer formation. These findings suggest that the stem region of HS6ST plays an important role in normal functioning, including the transit of HS6ST to the Golgi apparatus and maintaining the active conformation essential for enzyme activity.