Fusarium head blight is a disease of cereal crops caused by a group of trichothecene-producing Fusarium species. In the current study, three wheat genotypes with cv. Superb pedigree were evaluated for their ability to activate different defence-response pathways when exposed to one of three elicitors: (i) trichothecene-producing and (ii) non-producing F. graminearum strains, and (iii) the trichothecene toxin deoxynivalenol. Spikelets distal to the inoculation point were harvested at multiple time points in order to identify systemic temporal changes in transcript accumulation associated with resistance. Distinct differences were observed between the resistant genotypes and cv. Superb, as well as between the two resistant genotypes. The current data suggest that different molecular mechanisms exist not only between susceptibility and resistance responses, but between different forms of genetic resistance. It is proposed that Type 1 resistance in one of the resistant double haploid lines evaluated here involves a combination of structural features that slow fungal penetration and activation of a systemic response in uninfected tissues adjacent to the site of infection to prevent or minimize secondary infection; in contrast, Type 2 resistance is more likely a form of local resistance.