The on-line separation and structure elucidation of naphthodianthrones, flavonoids, and other constituents of an extract from Hypericum perforatum L. using high performance liquid chromatography (HPLC) coupled on-line with ultraviolet−visible, nuclear magnetic resonance (NMR), and mass spectrometry (MS) is described. A conventional reversed-phase HPLC system using ammonium acetate as the buffer substance in the eluent was used, and proton NMR spectra were obtained on a 500 MHz NMR instrument. The MS and MS/MS analyses were performed using negative electrospray ionization. In the present study, all of the major known constituents in extracts from Hypericum perforatum L. were identified, and two new substances which had not previously been reported as constituents of extracts of Hypericum perforatum L. were identified and their structures elucidated.