A common element in designed guidelines for assessment of the food safety of transgenic crops is centred on a comparative analytical analysis with conventionally bred crop plants, assuming that these products have a long history of safe use (i.e. OECD-principle of substantial equivalence). In this study we examine the utility of an off-line combination of 400 MHz proton (1H)-NMR spectroscopy and liquid chromatography (LC) for the multi-component comparison of low-molecular weight compounds (i.e. chemical fingerprinting) in complex plant matrices. The developed NMR-methodology can contribute to the demonstration of substantial equivalence by its ability to compare possible compositional alterations in a novel food crop with respect to related non-transgenic reference lines. In this respect a hierarchical approach is proposed by comparing the chemical fingerprints of the transgenic crop plant to those of: (1) isogenic parental or closely related lines bred at identical and multiple sites; (2) extended ranges of commercial varieties of that plant; and (3) downstream processing effects. This is of importance to assess the likelihood that some of the statistical differences in a transgenic crop plant may be false positives due to chance alone or arose from natural genetic and/or physiologic variations.