A new multiresidual LC-DAD-MS/MS method for the simultaneous detection of the major flavonoids and glycoalkaloids occurring in tomatoes has been developed and applied to the characterization of seven varieties of raw tomatoes grown in Italy and to their processed products. The new method allowed to determine rapidly the concentration of these secondary metabolites in a single analysis, showing that their content can be quite variable among the different varieties considered. On the contrary, a great depletion in glycoalkaloids and flavonoids is observed after processing, probably due to the harsh thermal treatment, which prevents the recognition of the varieties in the processed products.