The type III effector protein AvrPto acts as a virulence factor in susceptible plants lacking a cognate resistance gene but triggers hypersensitive response and disease resistance in tomato plants carrying the Pto gene or in tobacco plants carrying an unknown resistance gene. To assist the characterization of cellular responses caused by AvrPto in the plant, a pathogen-free system was adopted to isolate genes up-regulated 12 h after induced expression of AvrPto. By using subtraction cloning and transgenic tobacco plants expressing avrPto as a transgene, we isolated 125 nonredundant cDNA clones that represent avrPto-response genes (ARG). In addition to genes that are known to be induced by Pto-avrPto recognition, a number of new genes were also isolated. Most of ARG showed a specific induction in tobacco plants challenged with incompatible or nonhost pathogens. The use of an avrPto mutant that selectively eliminated the avrPto recognition in tobacco demonstrated that the ARG were induced in a highly specific manner by the avirulence, instead of the virulence activity of avrPto.