In this work, capillary electrophoresis time-of-flight mass spectrometry (CE-TOF-MS) is proposed to identify and quantify the main metabolites in three lines of genetically modified (GM) maize and their corresponding nontransgenic parental lines grown under identical conditions. The shotgun-like approach for metabolomics developed in this work includes optimization of metabolite extraction from GM and non-GM maize, separation by CE, online electrospray-TOF-MS analysis, and data evaluation. A large number of extraction procedures and background electrolytes are tested in order to obtain a highly reproducible and informative metabolomic profile. Thus, using this approach, significant differences were systematically observed between the detected amounts of some metabolites in conventional varieties (Aristis, Tietar, and PR33P66 maize) compared with their corresponding transgenic lines (Aristis Bt, Tietar Bt, and PR33P66 Bt maize). Results point to some of these metabolites as possible biomarkers of transgenic Bt maize, although a larger number of samples needs to be analyzed in order to validate this point. It is concluded that metabolomics procedures based on CE-TOF-MS can open new perspectives in the study of transgenic organisms in order to corroborate (or not) their substantial equivalence with their conventional counterparts.