The dothideomycete Stagonospora nodorum is a necrotrophic fungal pathogen of wheat and is the causal agent of Stagonospora nodorum blotch (SNB)1. This disease is responsible for over $100 million of yield losses in Australia annually. Recent studies have shown that this fungus produces a number of effector proteins that are internalised into host cells of susceptible wheat cultivars. The mechanism by which these effectors induce tissue necrosis in susceptible hosts is yet to be fully elucidated. We have applied a functional genomics approaches to elucidate the cellular processes leading to disease and provide insight into the mode-of-action of these effectors. Gas chromatography-mass spectrometry analysis of primary polar metabolites has been undertaken on tissue extracts and apoplastic fluid from SnToxA-infiltrated wheat. Results illustrate widespread perturbations in primary metabolism and reveal the first direct evidence of an increase in energy production in response to a pathogen effector. To further understand the host response to SnToxA at the secondary metabolism level, samples were also analysed using liquid chromatography-mass spectrometry. Our data indicate SnToxA causes an increase in defence-related secondary metabolites. These studies have also revealed the identity of a novel phytoalexin molecule that strongly inhibits the ability of Stagonospora nodorum to be able to sporulate. These complementary approaches have provided novel insight into the contribution of the SnToxA effector protein to SNB in wheat.