A UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase (polypeptide GalNAc transferase) cDNA was amplified from rat sublingual, submandibular and parotid glands, brain, skeletal muscle, and liver, using the polymerase chain reaction (PCR) and sequences derived from bovine polypeptide GalNAc transferase-Type 1 (polypeptide GalNAc transferase-T1). The transcripts encoding the rat sublingual gland and bovine enzymes were 91% identical in nucleotide sequence, except in their 5' and 3' untranslated regions. The enzymes encoded by the rat and bovine cDNAs were 559 amino acids in length and were virtually identical (98% amino acid sequence identity and 99.5% homologous overall). Northern blot analysis indicates that the polypeptide GalNAc transferase-T1 transcripts are expressed in many tissues but at widely differing levels. Although the amino acid sequence of polypeptide GalNAc transferase-T1 is conserved among mammals, the pattern of tissue expression varies between rats and humans. For example, the steady-state level of polypeptide GalNAc transferase-T1 transcript is quite low in lung relative to other rat tissues, whereas high expression of this transcript is detected in human lung. Therefore, we surmise that isoforms of polypeptide GalNAc transferase must exist and that isoforms are expressed in a tissue-dependent fashion. Searches of the GenBank database have revealed homologous sequences for several isoforms derived from several human tissues. In addition, hypothetical proteins from C. elegans also display strong homology; evidence suggests six ancestral isoforms of polypeptide GalNAc transferases may exist in C. elegans.