Abstract: Bacillus thuringiensis, which is a well-known and effective bio-insecticide, has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. Treatment of tomato roots with the “filter-sterilized cell-free filtrate” (CF) of B. thuringiensis systemically suppresses bacterial wilt caused by Ralstonia solanacearum through systemic activation of the plant defense system. Comparative analysis of the expression of the Pathogenesis-Related 1 [PR-1(P6)] gene, a marker for induced resistance to pathogens, in various tissues of tomato plants treated with the CF on their roots suggests that the B. thuringiensis-induced defense system is activated in the leaf, stem, and main root tissues, but not in the lateral root tissues. At the same time, the growth of R. solanacearum was significantly suppressed in the CF-treated main root tissue but not in the CF-treated lateral root tissues. This distinct activation of the defense reaction and suppression of R. solanacearum was reflected in differences in the transcriptional profiles in the main and lateral tissues in response to the CF. In the CF-treated main root tissue, but not CF-treated lateral root tissue, the expression of several salicylic acid (SA)-responsive defense-related genes was specifically induced, whereas jasmonic acid (JA)-related genes were specifically down-regulated in response to the CF. On the other hand, the induction of genes encoding ethylene (ET)-related proteins occurred equally in both main and lateral root tissues. Taken together, the co-activation of SA-dependent signaling pathway with ET-dependent signaling pathway and suppression of JA-dependent signaling pathway may play keys roles in B. thuringiensis-induced resistance to R. solanacearum in tomato plants.