ABSTRACTTo analyse cellular response to O3, the tolerant Arabidopsis thaliana genotype Col‐0 was exposed to O3 fumigation (300 ppb) for 6 h and the modulation of gene expression during the treatment (3 h after the beginning of the treatment, T3 h) and the recovery phase (6 h from the end of the treatment, T12 h) assessed by gene chip microarray and real‐time reverse transcriptase (RT)‐PCR analyses. The Arabidopsis transcriptional profile is complex, as new genes (i.e. reticuline oxidase) and pathways, other than those already reported as O3‐responsive, appear to be involved in the O3 response. The steady‐state transcript levels of several WRKY genes were increased in O3‐treated plants and the W‐box was the cis‐element over‐represented in the promoter region of T3 h up‐regulated genes. The fact that the W‐box element was also over‐represented in almost all T3 h‐induced receptor‐like kinases (RLKs) suggests a WRKY‐mediated control of RLKs under O3 stress and a mechanicistic similarity with the pathogen‐induced transcriptional responses. We investigated the molecular and physiological implications of our findings in relation to O3‐induced plant stress response.