Differential hybridization was used to isolate genes induced by viroid infection in tomato plants. Four new cDNA clones encoding a peroxidase, a desaturase-like enzyme, a lipoxygenase, and a proteinase inhibitor, were selected and characterized. All of these genes display a characteristic expression pattern, showing constitutive expression in roots of healthy plants and being ectopically activated in aerial tissues upon viroid infection and ethephon treatment. Possible functions for these genes in the viroid-tomato interaction are proposed. The existence of an integrated program that compiles developmental and defense-related responses is also suggested to explain the characteristic expression pattern detected for these genes as well as for other defense-related genes.