There is a growing interest in producing food plants with increased amounts of flavonoids because of their potential health benefits. Tomatoes contain small amounts of flavonoids, most of which are located in the peel of the fruit. It has been shown that flavonoid accumulation in tomato flesh, and hence an overall increase in flavonoid levels in tomato fruit, can be achieved by means of simultaneous overexpression of the maize transcription factors LC and C1. Fruit from progeny of two modified lines (2027 and 2059) was selected for a detailed analysis and individual identification of flavonoids, at different stages of maturity. Nine major flavonoids were detected in the flesh of transgenic ripe tomatoes. LC/NMR, LC/MS, and LC/MS/MS enabled us to identify these as kaempferol-3,7-di-O-glucoside (1), kaempferol-3-O-rutinoside-7-O-glucoside (2), two dihydrokaempferol-O-hexosides (3 and 4), rutin (5), kaempferol-3-O-rutinoside (6), kaempferol-3-O-glucoside (7), naringenin-7-O-glucoside (8) and naringenin chalcone (9), which were quantified by HPLC/DAD. All but 5, 6, and 9 were detected in tomato for the first time. The total flavonoid glycoside content of ripe transgenic tomatoes of line 2059 was about 10-fold higher than that of the controls, and kaempferol glycosides accounted for 60% of this. Kaempferol glycosides comprised around 5% of the flavonoid glycoside content of ripe control tomatoes (the rest was rutin and naringenin chalcone). The rutin concentration in both transgenic and control fruits was similar.