Silychristins A (1) and B (2), silydianin (3), silybins A (4) and B (5), and isosilybins A (6) and B (7) are major bioactive flavonolignans in silymarin, a herbal remedy derived from the milk thistle Silybum marianum. In this study, the seven major active flavonolignans including the diastereomers 1/ 2, 4/ 5, and 6/ 7 were completely separated using semi-micro-high performance liquid chromatography (HPLC) with a Nucleosil 100-3 C 18 HD column and a MeOH/water/formic acid mobile phase system. The collision-induced dissociation (CID) MS/MS and MS (3) spectra of these flavonolignans were studied systematically using hybrid ion-trap and time-of-flight (IT-TOF) mass spectrometry. Efficient differentiation between the seven flavonolignans (1- 7) was possible based on comparison of the resultant CID-MS/MS or MS (3) spectra. Each characteristic MS/MS or MS (3) fragmentation pattern was elucidated with high-resolution mass spectra by IT-TOF. The results with the present methodology show that liquid chromatography-mass spectrometry IT-TOF (LC-MS/IT-TOF) can be useful for general screening of active natural products from plant extracts and for the specific quality control of silymarin.