Metabolomic approaches were used to elucidate some key metabolite changes occurring during interactions of Magnaporthe grisea– the cause of rice blast disease – with an alternate host, Brachypodium distachyon. Fourier-transform infrared (FT-IR) spectroscopy provided a high-throughput metabolic fingerprint of M. grisea interacting with the B. distachyon accessions ABR1 (susceptible) and ABR5 (resistant). Principal component– discriminant function analysis (PC-DFA) allowed the differentiation between developing disease symptoms and host resistance. Alignment of projected ‘test-set’ on to ‘training-set’ data indicated that our experimental approach produced highly reproducible data. Examination of PC-DFA loading plots indicated that fatty acids were one chemical group that discriminated between responses by ABR1 and ABR5 to M. grisea. To identify these, non-polar extracts of M. grisea-challenged B. distachyon were directly infused into an electrospray ionization mass spectrometer (ESI-MS). PC-DFA indicated that M. grisea-challenged ABR1 and ABR5 were differentially clustered away from healthy material. Subtraction spectra and PC-DFA loadings plots revealed discriminatory analytes (m/z) between each interaction and seven metabolites were subsequently identified as phospholipids (PLs) by ESI-MS-MS. Phosphatidyl glycerol (PG) PLs were suppressed during both resistant and susceptible responses. By contrast, different phosphatidic acid PLs either increased or were reduced during resistance or during disease development. This suggests considerable and differential PL processing of membrane lipids during each interaction which may be associated with the elaboration/suppression of defence mechanisms or developing disease symptoms.