Liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (LC-MS/APCI) with a chiral phase was used for separation of triacylglycerols (TAG) obtained either by organic synthesis or isolated from different algal species. We present chromatographic characteristics and tandem mass spectra of enantiomers and positional isomers (regioisomers) of C16, C18 and C20 polyunsaturated fatty acids. The retention time was found to depend on the structure of the given TAG, increasing with increasing number of double bonds and decreasing with increasing number of the carbons in TAG, with the exception of dieicosapentaenoyl-palmitoyl-glycerols.