Fusarium graminearum causes Fusarium head blight (FHB) and Fusarium root rot (FRR) in small-grain cereals. The host response to FRR and the transcriptome responses differences of FHB and FRR are not well studied. Using the model Brachypodium distachyon (Bd), the RNA-seq transcriptome response of Bd to F. graminearum (Fg) infection of heads and roots was carried out. Additionally, the RNA-seq transcriptome response and predicted secretome within the same infected material were performed against in vitro samples of Fg.