Structured lipids containing special fatty acids were produced via lipase-catalyzed interesterification. Chromatographic methods were modified for the analysis of the acylglycerol content of the selected interesterified products, resulting from different reacting substrate mixtures and reaction systems. A modified normal-phase high performance liquid chromatographic method with evaporative light-scattering detection was used in the analysis of the diacylglycerols formed as intermediate products during interesterification. One of the advantages of the method was the low solvent consumption through the use of a narrow-bore silica column. Another advantage was in the speed of the analysis. Using a suitable solvent gradient, both diacylglycerol and triacylglycerol components were separated by reversed-phase high performance liquid chromatography within 50 min, providing both the diacylglycerol content and the triacylglycerol composition. High-temperature gas chromatography was also used to separate both diacylglycerol and triacylglycerol molecular species after trimethylsilylation of the structured lipid samples. Good agreements in the values obtained for the concentrations of diacylglycerols and the triacylglycerol compositions were apparent with the different chromatographic methods.