We have isolated overlapping cDNA clones representing the full-length transcript (4038 base pairs) for murine beta-1,4-galactosyltransferase. The coding sequence predicts a membrane-bound glycoprotein with 3 distinct structural features: 1) a large, potentially glycosylated COOH-terminal domain (355 amino acids) which is positioned within the Golgi lumen and contains both the catalytic and alpha-lactalbumin binding site; 2) a single transmembrane domain (20 amino acids); and 3) a short NH2-terminal domain containing 2 Met residues, separated by 12 amino acids. The gene for murine beta-1,4-galactosyltransferase is unusual in that it specifies 2 mRNA transcripts which differ in length by about 200 base pairs. The longer transcript contains both Met residues found in the NH2-terminal domain; the shorter transcript contains only the downstream Met. These results predict that 2 related forms of beta-1,4-galactosyltransferase of 399 and 386 amino acids are synthesized as a consequence of alternative translation initiation. Both forms of the enzyme are identical in primary structure with the exception that the long form has an NH2-terminal extension of 13 amino acids which, in part, potentially encodes a cleavable signal sequence. The structural implications, topological distribution and potential biological significance of the 2 forms of the enzyme are discussed.