In this study, the major carotenoids (beta-carotene and lycopene) present in tomato fruits were analyzed by CEC with a methacrylate ester-based monolithic column. The effects of the porogenic solvent ratio, and the hydrophobicity of bulk monomer employed were examined on carotenoids separations. A fast separation of these analytes was achieved in less than 5.0 min in a mobile phase containing 35% THF, 30% ACN, 30% methanol, and 5% of a 5 mM Tris aqueous buffer, pH 8, with lauryl methacrylate-based monoliths. The CEC method was evaluated in terms of detection limit and reproducibility (retention time, area, and column preparation) with values below 1.6 mu g/mL and 7.2%, respectively. The proposed procedure was successfully applied to the determination of both carotenoids in fruits of several tomato-related species and its usefulness to analyze large series of samples for nutritional quality screening trials in tomato breeding programs is demonstrated. To our knowledge, this is the first work that exploits the powerful and user-friendly monolithic technology for quality breeding and germplasm evaluation program purposes.