UDP-N-acetylglucosamine:lysosomal-enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase) catalyzes the initial step in the synthesis of the mannose 6-phosphate determinant required for efficient intracellular targeting of newly synthesized lysosomal hydrolases to the lysosome. The enzyme was partially purified ϳ30,000-fold by chromatography of solubilized membrane proteins from lactating bovine mammary glands on DEAE-Sepharose, reactive green 19-agarose, and Superose 6. The partially purified enzyme was used to generate a panel of murine monoclonal antibodies. The antiGlcNAc-phosphotransferase monoclonal antibody PT18 was coupled to a solid support and used to immunopurify the enzyme ϳ480,000-fold to apparent homogeneity with an overall yield of 29%. The purified enzyme has a specific activity of 10-12 mol of GlcNAc phosphate transferred per h/mg using 100 mM ␣-methylmannoside as acceptor.The subunit structure of the enzyme was determined using a combination of analytical gel filtration chromatography, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and amino-terminal sequencing. The data indicate that bovine GlcNAc-phosphotransferase is a 540,000-Da complex composed of disulfide-linked homodimers of 166,000-and 51,000-Da subunits and two identical, noncovalently associated 56,000-Da subunits.The trafficking of most lysosomal hydrolases in higher eucaryotes is mediated by a mannose 6-phosphate-dependent pathway. Asparagine-linked oligosaccharides on newly synthesized lysosomal hydrolases are sequentially modified by two enzymes to generate a mannose 6-phosphate recognition marker. The initial and determining step in the biosynthesis of the mannose 6-phosphate recognition marker is catalyzed by the enzyme UDP-N-acetylglucosamine:lysosomal-enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase).