The application of high-performance liquid chromatography on-line coupled with atmospheric-pressure chemical-ionization mass spectrometry (HPLC-APCI-MS), electrospray-ionization mass spectrometry (ESI-MS), as well as with tandem mass spectrometry (MS/MS), for the analysis of natural products is discussed. The separation, detection and structure elucidation of polyamine-containing compounds contained in plant material and spider venoms was performed by means of these techniques. The use of the methods for biochemical investigations of diverse natural materials is proposed.