Advantages and disadvantages of combined extraction and separation techniques for isolation of secondary metabolites in plant materials are discussed. The number of identified substances in crude extracts is often reduced due to co-elution of two or more compounds. Purification procedures are necessary for more detailed studies due to interference of other substances. Solid-phase extraction (SPE) is the most useful extraction procedure. Its advantages in the purification, especially for more precise identification of isoflavones, are presented. Application of HPLC/DAD/MS tandem to identification and structure characterization of isoflavones in plant materials is described. The presence of six isoflavone glycoside acetates and of eight malonates in Trifolium pratense was confirmed by HPLC-MS. Biosynthesis of flavonoids is described. Combination of SPE and HPLC-DAD-MS techniques improves the procedures and allows more precise identification of secondary metabolites due to reduced interferences and co-elution of other compounds. Application of SPE leads to simpler chromatograms but the sensitivity is sacrificed.