Sugarcane (Saccharum officinarum L., Gramineae) bagasse and leaves were investigated for their flavonoid content and transgenic sugarcane ("Bowman-Birk" and "Kunitz") was compared with non-modified ("control") plants. Analyses were carried out by high-performance liquid chromatography coupled to diode array UV detection (LC/UV), also using post-column addition of shift reagents, and tandem MS (atmospheric pressure chemical ionization-MS/MS and collision-induced dissociation-MS). On-line UV and MS data demonstrated the presence of methoxyflavone glycosides and aglycones in a total of seven compounds. Three naturally occurring flavones glycosides and two unusual erythro- and threo-diastereoisomeric flavolignan 7-O-glucosides were identified together with their aglycones.