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. This comprehensive survey of global gene expression in response to colonization by a virulent fungal isolate constitutes an important resource that should help us to further our understanding of the rice blast disease process.