An optimized method using liquid chromatography coupled with electrospray ionization ion trap mass spectrometry (LC/ESI-ITMS) in negative ion mode has been developed for screening different structural classes of intact glucosinolates in six Chinese medicinal herbs. The glucosinolates were extracted with hot methanol/water (70:30 v/v) and separation of the individual glucosinolates was achieved using a reversed-phase C18 column with an aqueous ammonium acetate/methanol gradient. Identification of the intact glucosinolates was based on the detection of compounds with a constant neutral loss of 242 Da corresponding to the combined loss of anhydroglucose (162 Da) and sulfur trioxide (80 Da) in collision-induced dissociation. The structures of the identified glucosinolates were confirmed with the use of group-specific product ions at m/z 195, 241, 259, 275 in their corresponding MS/MS product ion spectra. Differentiation of intact glucosinolates was achieved through their respective retention times and molecular masses as well as the characteristic product ions. The limits of detection were at the low nanogram level per injection, based on constant neutral loss scans. Significant variation in the compositions of intact glucosinolates was identified in the cruciferous herbs. This method was applied in the differentiation and quality control of two pairs of easily confused herbs.