Commercial by supplied triacylglycerols and synthesized triacylglycerols were used in this project. Analysed triacylglycerols with the range of carbon number (CN) 24–54 consisted of saturated and unsaturated fatty acids. Two capillary columns were used in the analyses of triacylglycerols, namely non-polar (Optima^®-1-TG) and medium polar (Optima^®-17-TG) types. In this study the effectiveness of separation (A) of triacylglycerols with different carbon number values, (B) of triacylglycerols with different unsaturation degree, (C) of positional isomers were determined and further possibilities to separate another lipid compounds were analysed. The column Optima^®-17-TG separates TAG according to the degree of unsaturation while the column Optima^®-1-TG separates saturated and unsaturated TAG. High temperature capillary gas chromatography was used to determine changes in triacylglycerol composition during the transesterification of structured fats.