The gram-negative bacterium Xylella fastidiosa (Xf) is the causal agent of Pierce's disease (PD) in grape. This disease is vectored by xylem-feeding insects and continues to cause serious vineyard losses in California. PD resistant plants produced by classical or molecular breeding techniques are the ultimate solution to this disease. However, information regarding genetic control of resistance is limited and the molecular basis of resistance mechanisms to PD is unknown. Transcriptomes (5,794 ESTs) from 12 tissue specific (stem, leaf, and shoot) subtractive suppression hybridization cDNA libraries were obtained and characterized from a highly resistant and highly susceptible sibling genotype (Vitis rupestris x V. arizonica). Further, genome-wide transcriptional profiling using a custom high-density (382,900 probes) microarray chip of 20,020 Vitis transcripts showed significant variations in responses between the susceptible and resistant genotypes to Xf infection. Differentially expressed transcripts reflecting spatial and temporal responses to PD involved in metabolic processes such as diseases resistance, water stress, photosynthesis, and cell wall synthesis were identified. In conclusion, the Vitis responses to Xf are genotype and tissue dependent, and are stage specific.