Verticillium dahliae is a soil-borne vascular pathogen that causes severe wilt symptoms in a wide range of plants. Co-culture of the fungus with Arabidopsis roots for 24 hours induces many changes in the gene expression profiles of both partners, even before defense-related phytohormone levels are induced in the plant. Both partners reprogram sugar and amino acid metabolism, activate genes for signal perception and transduction, and induce defense and stress responsive genes. Furthermore, analysis of Arabidopsis expression profiles suggests a redirection from growth to defense. The plant and fungal genes that rapidly respond to the presence of the partner might be crucial for early recognition steps and the future development of the interaction. Thus they are potential targets for the control of V. dahliae-induced wilt diseases. Overall design: The aim of this study was to identify important targets regulated in both partners in the initial phase of interaction (24h). After 24 h of co-cultivation the fungus colonizes the plant root and first penetration of plant tissue by the fungus is visible while the vascular tissue of the plant is not yet colonized (pre-vascular phase).