Agrobacterium tumefaciens - Arabidopsis thaliana provides an excellent model system to study bacterial pathogenesis and plant interactions. It is well established that, upon recognizing plant-derived signals, A. tumefaciens activates its virulence programing, culminated by the transfer and integration of T-DNA into the plant genome. However, the initial signaling and response of the plant host during A. tumefaciens -plant interactions is less understood. In this study, A. thaliana were co-cultivated (infected) with A. tumefaciens in a sterile hydroponic system for 8 h, and the transcriptome profiles of root and shoot were determined by microarray analysis. Overall, hundreds of genes involved in plant responses to stress, regulation of transcription, signal transduction or plant metabolism are differentially expressed in roots and shoots upon A. tumefaciens infection. In total, 323 genes were up-regulated and 226 were down-regulated by a log2 transformed fold change of at least 2 in roots upon A. tumefaciens infection, as compared with mock-inoculated plants. In the shoot, 249 genes were up-regulated and 152 were down-regulated in response to A. tumefaciens infection in the roots. Functional classification and comparative analysis revealed that, in response to pathogen attack, the host plant demonstrated significantly differential signaling loops between locally (roots) and distally (shoots) affected sites, despite of little overlap between transcriptome responses. Upon A. tumefaciens infection, roots displayed a strong induction of defense and hormone signaling pathways involving salicylic acid, abscisic acid, ethylene, and auxins, which play essential roles in plant acclimation responses in the root. On the contrary, jasmonic acid and gibberellic acid signaling processes were most activated in the shoots. The identification of genes and signaling pathways that are differentially regulated in roots and shoots may serve as possible targets in molecular breeding for disease tolerant plants or for improving Agrobacterium-mediated plant transformation.