Phosphatidylethanolamine N-methyltransferase (PEMT) catalyzes the conversion of phosphatidylethanolamine (PE) to phosphatidylcholine (PC) in a series of three methylation reactions. Preliminary studies of PEMT in humans led to the cloning of three cDNAs each of which has a different 5' untranslated region (5'UTR). To determine the origin of PEMT splice variants and to investigate expression of the gene in human liver, we isolated a bacterial artificial chromosome (BAC) clone containing the full-length human gene. Each of the three unique untranslated first exons is present in a contiguous array in the gene, confirming the integrity of the cDNAs and alternative processing of PEMT transcripts. Human liver, heart and testis contain the highest levels of PEMT transcripts and of these, liver has the greatest PEMT expression. Furthermore, each of the three PEMT transcripts is present in varying abundance in liver whereas heart and testis contain only one and two transcripts, respectively. Thus, differential promoter usage in the human PEMT gene generates three unique transcripts and confers a tissue-specific expression pattern.