The citrus canker disease, caused by Xanthomonas axonopodis pv. citri (Xac), has emerged as one of the major threats to the brazilian citriculture because it affects all commercial citrus varieties, decreases the production and quality of the fruits and can spread rapidly in the citrus growing areas. The symptoms include canker lesions, leading to abscission of fruits and leaves and general tree decline. Within the genus Xanthomonas, several genes have been found associated with pathogenecity and virulence. However, little is known about the mechanisms involved in the Xac- Citrus interaction and the development of the canker disease. In this work we analyzed the differential expression of genes involved in the development of the canker disease in citrus leaves (Citrus sinensis) in response to Xac infection. Therefore we constructed two Supression Subtracted Hybridization libraries (SSH) with mRNA from leaves infiltrated with Xac or water after 10 days of inoculation. The libraries were screnned by dot blot and the 17 differentially expressed genes were sequenced and identified through BLAST searches against the Citrus EST databases. The differential gene expression was evaluated by northern blot and Real Time PCR (RT PCR). To complement our data, the expression of the 17 genes was compared in cDNA samples from citrus leaves that had been infiltrated with Xac, water or Xanthomonas axonopodis pv. aurantifolii (Xaa), wich is not pathogenic to orange but causes canker in lemon. Our results show that Xac and Xaa induce and repress a similar set of genes, however at different levels. We found that both pathogens altered the pathways of auxin transport, gibberellins and terpene synthesis, vesicle trafficking and transport, cell cycle and protein synthesis, photorespiration and disease response. The analyses of these genes will be of great importance to understand the events triggering the development of the canker symptoms.