In this work, the potential of combining capillary electrophoresis-time-of-flight-mass spectrometry (CE-TOF-MS) and Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS) for metabolomics of genetically modified organisms (GMOs) is demonstrated. Thus, six different varieties of maize, three of them transgenic (PR33P66 Bt, Tietar Bt and Aristis Bt) and their corresponding isogenic lines (PR33P66, Tietar and Aristis) grown under the same field conditions, were analyzed. Based on the ultrahigh resolution and remarkable mass accuracy provided by the 12-T FT-ICR-MS it was possible to directly analyze a good number of metabolites whose identity could be proposed based on their specific isotopic pattern. For identification of metabolite isomers, CE-TOF-MS was also used combining the information on nominal mass with electrophoretic mobility corroborating in that way the identity of several new biomarkers. Furthermore, PLE extractions were evaluated in order to establish selective extraction as an additional criterion to obtain useful information in maize metabolomics. Differences in the metabolite levels were found between the three transgenic maize varieties compared with their wild isogenic lines in some specific metabolic pathways. To our knowledge, this is the first time that an approach as the one presented in this work (pressurized liquid extraction+FT-ICR-MS+CE-TOF-MS) is shown for a metabolomic study.