A metabolite profiling methodology was developed using rice as model crop. The approach is based on consecutive extraction of lipids and polar compounds and subsequent fractionations of both extracts. Transesterification-solid phase extraction (lipids) and selective hydrolysis of silylated derivatives (polar compounds) are applied to separate major from minor constituents. The method covers a broad spectrum of chemical classes. Preliminary investigation of the four fractions by gas chromatography/ mass spectrometry (GC/MS) analysis of silylated derivatives identified more than 100 compounds. This unbiased approach can serve as an additional analytical tool for the safety assessment of genetically modified crops and may help to increase the chance to detect unintended effects due to the application of recombinant DNA techniques.