CTP:phosphoethanolamine cytidylyltransferase (Pcyt2) catalyzes the rate-controlling reaction of the CDPethanolamine (Kennedy) pathway. We have previously established that Pcyt2 is encoded by a single gene that can be alternatively spliced from an internal exon into two transcripts, designated Pcyt2a and Pcyt2b. Little is currently known about the regulation of Pcyt2. Here, we functionally express both murine Pcyt2 (mPcyt2) transcripts and investigate the roles of the two proteins in the regulation of mPcyt2 activity. We demonstrate that the tagged and purified a and b proteins differ significantly in their kinetic properties. The K m of mPcyt2a for phosphoethanolamine was 318.4 mM, compared with 140.3 mM for mPcyt2b. The maximal velocities of the a and b isoforms at saturating conditions for both substrates were 138.0 and 114.4 nmol/ min/mmol enzyme, respectively. When phosphoethanolamine was used at a fixed concentration of 1 mM, the K m of mPcyt2a for CTP was 102.0 mM and that of mPcyt2b was 84.09 mM. Using a combination of nondenaturing PAGE, gel filtration chromatography, and immunoprecipitation, we provide evidence that mPcyt2a and mPcyt2b proteins can form both homodimeric and heterodimeric complexes. We show that alternative splicing of the mPcyt2 transcript is ubiquitous but could also be regulated in a tissue-specific manner, producing a variable ratio of mPcyt2a/mPcyt2b mRNAs. The expression of two distinct protein isoforms maybe an important mechanism by which Pcyt2 activity is regulated.-Tie, A., and M. Bakovic. Alternative splicing of CTP:phosphoethanolamine cytidylyltransferase produces two isoforms that differ in catalytic properties. J. Lipid Res. 2007Res. . 48: 2172Res. -2181