We cloned in silico a novel human UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase (pp-GalNAc-T), pp-GalNAc-T12. The deduced amino acid sequence of pp-GalNAc-T12 contains all conserved motifs in pp-GalNAc-T family proteins. Quantitative real time polymerase chain reaction analysis revealed that the pp-GalNAc-T12 transcript was expressed mainly in digestive organs such as stomach, small intestine and colon. The recombinant pp-GalNAc-T12 transferred GalNAc to the mucin-derived peptides such as the Muc1a, Muc5AC, EA2 peptides and the GalNAc-Muc5AC glycopeptide. Since mucins are glycoproteins mainly produced in the digestive organs, our results suggest that pp-GalNAc-T12 plays an important role in the initial step of mucin-type oligosaccharide biosynthesis in digestive organs.