Maize ( Zea mays ) kernels grown conventionally and organically, respectively, were investigated using a gas chromatography/mass spectrometry (GC/MS)-based metabolite profiling methodology. By analysis of three cultivars grown at two locations with different input systems and at a third location where both organic and conventional farming were applied, the impact of the growing regime on the metabolite spectrum should be put into the context of natural variability. The applied analytical approach involved consecutive extraction of freeze-dried maize flour and subsequent subfractionation. Approximately 300 compounds from a broad spectrum of chemical classes were detected, of which 167 were identified. The metabolite profiling data were statistically assessed via principal component analysis (PCA) and analysis of variance (ANOVA). The PCA demonstrated that the observed separations were mainly due to genetic differences (cultivars) and environmental influences. The different input systems (conventional/organic) only led to minor differentiations. ANOVA and quantification of selected constituents confirmed these observations. Only three metabolites (malic acid, myo-inositol, and phosphate) were consistently different because of the employed input system if samples from all field trials were considered.