Whereas the molecular events associated with disease resistance are largely studied, those occurring in susceptible plants are poorly known, especially in Monocots. We chose the rice/Magnaporthe grisea system to explore the molecular modifications that are induced in susceptible plant tissues following pathogen attack. A truly compatible interaction (between O. sativa cultivar Nipponbare and M. grisea isolate FR13) at time points where infection occurs without visible symptoms was studied. Changes in rice transcript levels at 3 and 4 days post inoculation were measured using Affymetrix chips. In addition to the up-regulation of a large number of defence-related genes, this analysis revealed new features indicating extensive reprogramming of host gene expression. Microarray expression data were confirmed for 35/38 genes using quantitative RT-PCR, thus demonstrating the robustness of these transcript profiling experiments. Transcript levels were compared in a compatible versus an incompatible interaction. Auxin and abscisic acid responsive genes were induced preferentially in the compatible interaction, suggesting that M. grisea may repress host defences via manipulation of these plant hormone signalling pathways. This comprehensive survey of global gene expression in response to colonization by a virulent fungal isolate constitutes an important resource that should help us gain a better understanding of the rice blast disease process.