Abstract The presence of relatively high concentrations of plasmalogen choline and ethanolamine in the heart of many animal species suggests a role of these ether-linked phospholipids in the pathophysiology of certain myocardial diseases. However, the fatty acid composition of myocardial plasmalogens in many species is not known. This study examined the fatty acid composition of the choline and ethanolamine glycerophospholipids in pig heart and compared the results with those in rat heart. Lipids were extracted from the heart biopsies obtained from pig and rat by standard techniques. Phosphoglycerides were separated by thin-layer chromatography followed by their derivatization into fatty acid methyl esters (FAMEs) and dimethyl acetals (DMAs). FAME and DMA samples were analyzed using gas chromatography-mass spectroscopy. Our results indicate striking differences in the fatty acid composition of both choline and ethanolamine glycerophosphates between rat heart and pig heart. Pig heart ethanolamine glycerophosphates are rich in linoleic acid (18:2) and arachidonic acid (20:4). but low in descosahexenoic (22:6) fatty acids while choline glycerophosphates are poor in both 20:4 and 22:6 fatty acids compared to those in rat hearts.