TGN38 and TGN41 are isoforms of an integral membrane protein that is predominantly localized to the trans-Golgi network (TGN) in rat cells. They have been proposed to form a heterodimer and to be involved in the budding of exocytic transport vesicles from the TGN. By cDNA cloning and analysis using polymerase chain reaction, we found that there were two TGN38 isoforms in a strain of mouse (ICR), whereas other strains examined (BALB/c, DBA/2, and C57BL/6) had only one TGN38. The major difference between the two isoforms was in the number of characteristic octapeptide repeats. Apart from this, there were several nucleotide substitutions between them. The two isoforms appeared to be derived from two distinct genes but not from one gene via alternative splicing. Furthermore, we failed to show the presence of TGN41 in all the strains examined. This result suggests that TGN38 may function as a monomer or a homodimer in mouse cells.