Metabolomics is a post genomic technology which seeks to provide a comprehensive profile of all the metabolites present in a biological sample. This complements the mRNA profiles provided by microarrays, and the protein profiles provided by proteomics. To test the power of metabolome analysis we selected the problem of discrimating between related genotypes of Arabidopsis. Specifically, the problem tackled was to discrimate between two background genotypes (Col0 and C24) and, more significantly, the offspring produced by the crossbreeding of these two lines, the progeny (whose genotypes would differ only in their maternally inherited mitichondia and chloroplasts).