Abstract: In order to determine the effect of aphid (Myzus persicae) feeding and infection withpotato leafroll virus (PLRV) on the metabolism of potato (Solanum tuberosum) plants, twosequential trials were designed and carried out, followed by a molecular-chemicalcharacterization of the tissue (leaves) of the plants using Pyrolysis-Field Ionisation MassSpectrometry (Py-FIMS). Thus the comparison of the samples is based on the application ofpattern-recognition techniques in combination with multivariate statistics. The m/z-signals ofhighest discriminative power indicate the molecular-chemical diversity. In the first experimentwe tested the effects of aphid feeding and virus infection. The discriminant analysis resulted in acomplete separation of the treatments. The second experiment provided evidence of the effects ofgrafting and transgenes, but there were fewer significant differences in the m/z-signals than in thefirst experiment. As a consequence, separation of the sample sets by only one factor wasimpossible. The m/z-signals of highest discriminating power were evaluated and verified and themajority were tentatively assigned to marker signals of isoprenoids, which are associated withplant defence and aphid and/or virus modulated metabolism.