The application of capillary HPLC/continuous-flow liquid secondary ion mass spectrometry (CF-LSIMS) as part of an integrated approach for characterizing discovery stage in vitro metabolites, using a specific inhibitor for 5-lipoxygenase as a model compound, was investigated. CF-LSIMS demonstrated excellent sensitivity in detecting the metabolites in both the positive and the negative ion modes, with a good full-scan mass spectrum obtained when 5 pmol of metabolite was injected onto the capillary column. Strong pseudomolecular ions and key fragment ions were observed in the primary spectra of the parent drug and its three oxidative in vitro metabolites, allowing the site of metabolism to be pinpointed to particular substructures. This technique demonstrated versatility and offered a very rapid screening procedure for metabolite identification.