A microdialysis (MD) sampling coupled with electrospray ionization linear quadrupole ion trap mass spectrometry (LTQ-MS(n)) method has been developed for rapid and sensitive analysis of rat microdialysate metabolite profile of Fructus Corni, a well-known Traditional Chinese Medicine (TCM). The purified samples were separated by a reversed-phase HPLC with C₁₈ column under a gradient elution. Parent compounds and metabolites of crude and processed Fructus Corni of Jiu Zheng Pin (JZP, JZP is produced after steaming the crude drug pre-steeped in wine) were detected by the on-line MS(n) detector in negative scan model. The identification of the metabolites and their structural elucidation were performed by comparing the changes in molecular mass and defining sites of biotransformation based on the accurate MS(n) spectral information of diagnostic fragment ions. In this work, we used such strategies for the identification of the parent compounds and metabolites of crude and processed Fructus Corni in rats, and seven parent compounds and three new metabolites of Fructus Corni were found in rats for the first time. This study provides important structural information regarding to the metabolism of crude Fructus Corni and its JZP. Furthermore, this work also demonstrated the possibilities of using microdialysis sampling coupled with LC-MS(n) approach for identification of bioactive compounds from TCM in vivo. Copyright © 2011 Elsevier B.V. All rights reserved.