Minute samples of xylem from healthy and Fusarium oxysporum f.sp. dianthi-infected stems of carnation cultivars differing in degree of resistance to F. oxysporum were investigated by in-source pyrolysis low voltage EI mass spectrometry and by pyrolysis under ammonia CI conditions. Healthy xylem of both cultivars showed PY-MS spectra with markers for cellulose, hemicelluloses, phenolic acids, and a mixed guaiacyl-syringyl lignin. At different stages of infection visibly infected, brown coloured, xylem was separated under the microscope from healthy-looking parts. The PY-MS spectra of the diseased xylem of susceptible ‘Lena’ were entirely different from those of healthy(-looking) areas, showing a drastic change in lignin pyrolysis product distributions. In most cases practically all syringyl constituents, both mono- and dimeric, had disappeared. In some cases also an overall decrease in relative intensity of the lignin pyrolysis products was observed. Invasion of the fungus thus induced a major change of cell wall composition as a result of lignin degradation along different pathways: demethoxylation of syringyl units, the major pathway in ‘Lena’, and propenyl side chain oxidation. The PY-MS spectra of infected ‘Novada’ generally showed the overall oxidation of lignin and less demethoxylation. The ‘Novada’ spectrum also showed m/z 239, 287, and an increase of 257 and 271, which are molecular ions indicative of the phytoalexins dianthalexin and the dianthramides methoxydianthramide S, hydroxydianthramide B and methoxydianthramide B. The compounds appeared comparatively volatile and therefore could be desorbed as a thermal extract before other pyrolysis fragments appear. The compounds were practically absent in adjacent, healthy looking, xylem. Low voltage EI MS of methanol extracts of about 2 mm 3 of infected ‘Novada’ xylem confirmed these data and in a single case also showed evidence for hydroxyanthranilic acid ( m/z 153) which is attributed to degradation of dianthramine. Spectra of thermal and methanolic extracts were quite similar.