The chemical profiling of illicit drugs is an important analytical tool to support the work of investigating and law enforcement authorities. In our work, comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) combined with nontargeted, pixel-based data analysis was adapted for the chemical profiling of 3,4-methylenedioxymethamphetamine (MDMA). The validity and benefit of this approach was evaluated by analyzing a well-investigated set of MDMA samples. Samples were prepared according to a harmonized extraction protocol to ensure the comparability of the chemical signatures. The nontargeted approach comprises preprocessing followed by analysis of variances as a fast filter algorithm for selection of a variable subset followed by partial least squares discriminant analysis for reduction to promising marker compounds for discrimination of the samples according to their chemical profile. Forty-seven potential marker compounds were determined, covering most of the target impurities known from the harmonized one-dimensional profiling as well as other compounds not previously elucidated.