Porous particles of 1.7 microm was employed for ultra high performance liquid chromatography (UPLC), resulting in higher peak capacity, greater resolution and increased sensitivity in comparison with high performance liquid chromatography (HPLC). Time-of-flight mass spectrometer (TOF-MS) with a lockmass interface was used for the structure identification through exact mass and MS/MS experiment. The hyphenation of these two technologies made it a suitable platform for analysis of complex samples and identification of unknown compounds. Ginsenoside Rg3 has been considered as the major active component of Panax ginseng. Effect of the administration of a single dose of the Ginsenoside Rg3 to male Sprague Dawley rats on the urinary metabolite profiles of a range of endogenous metabolites had been investigated using UPLC/TOF-MS. Urine samples were collected from both dosed and control animals. Analysis of these samples revealed marked changes in the pattern of endogenous metabolites due to the effect of Ginsenoside Rg3. Significant disturbances in the urinary metabolite were observed in the first day after dose. Endogenous metabolites with significant up-regulation identified by accurate mass and MS/MS were xanthurenic acid, and kynurenic acid.