Bacterial wilt is a common disease that causes severe yield and quality losses in many plants. In the present study, we used the model Ralstonia solanacearum-Arabidopsis thaliana pathosystem to study transcriptional changes associated with wilt disease development. Susceptible Col-5 plants and RRS1-R-containing resistant Nd-1 plants were root-inoculated with R. solanacearum strains harbouring or lacking the matching PopP2 avirulence gene. Gene expression was marginally affected in leaves during the early stages of infection. Major changes in transcript levels took place between 4 and 5 days after pathogen inoculation, at the onset of appearance of wilt symptoms. Up-regulated genes in diseased plants included ABA-, senescence- and basal resistance-associated genes. The influence of the plant genetic background on disease-associated gene expression is weak although some genes appeared to be specifically up-regulated in Nd-1 plants. Inactivation of some disease-associated genes led to alterations in the plant responses to a virulent strain of the pathogen. In contrast to other pathosystems, very little overlap in gene expression was detected between the early phases of the resistance response and the late stages of disease development. This observation may be explained by the fact that above-ground tissues were sampled for profiling whereas the bacteria were applied to root tissues. This exhaustive analysis of Arabidopsis genes whose expression is modulated during bacterial wilt development paves the way for dissecting plant networks activated by recognition of R. solanacearum effectors in susceptible plants.