In recent years, a family of five GlcNAc-6-O-sulfotransferases, called the GlcNAc6STs, has been molecularly cloned. One of these, GlcNAc6ST-2 (originally named HEC-GlcNAc6ST or LSST), shows a very restricted expression at the mRNA level in high endothelial cells (HECs) of lymph nodes high endothelial venules (HEVs). This enzyme has been shown to be involved in elaborating the 6-sulfo sLex structure on a set of mucin-like acceptors within HECs, thus providing a critical recognition determinant for L-selectin during the process of lymphocyte homing to lymph nodes. Limited information has been available about the closely related sulfotransferase known as GlcNAc6ST-3 (I-GlcNAc6ST). Here, employing transfection experiments with a series of glycoprotein acceptors, we report that this sulfotransferase has a marked preference for sulfating O-linked sugars of mucin-type acceptors, whereas other sulfotransferases in the family (GlcNAc6ST-1, GlcNAc6ST-2) and a Gal-6-O-sulfotransferase exhibit strong activity on both mucin-type acceptors and glycoproteins with predominantly N-linked chains. PCR analysis of cDNAs derived from a panel of tissues and purified cell populations confirms the strong expression of GlcNAc6ST-3 in gut-associated tissues and extends the expression to include lymphocytes. In contrast to GlcNAc6ST-2, GlcNAc6ST-3 transcripts are present minimally, if at all, in HECs; moreover, this enzyme is not able to generate the 6-sulfo sLex epitope in transfected cells. These latter findings argue that GlcNAc6ST-3 is not involved in generating HEV-expressed ligands for L-selectin.