Triterpenes are one of the largest classes of plant natural products, with an enormous variety in structure and bioactivities. Here, triterpene saponins from hairy roots of the model legume Medicago truncatula were profiled with reversed-phase liquid chromatography coupled to negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (LC ESI FT-ICR MS). Owing to the accuracy of the FT-ICR MS, reliable molecular formulas of the detected compounds could be predicted, which, together with the generated MS(n) spectra, allowed the tentative identification of 79 different saponins, of which 61 had not been detected previously in M. truncatula. Upon collision-induced dissociation of saponins that contain a uronic acid residue in the sugar chain, fragment ions resulting from cross-ring cleavages of the uronic acid residues were observed. The identified saponins are glycosides of 10 different sapogenins, of which three were not detected before in M. truncatula. Zanhic acid glycosides, which are prevalent in the aerial parts of M. truncatula, were absent in the hairy root extracts. This metabolite compendium will facilitate future functional genomic studies of triterpene saponin biosynthesis in M. truncatula.