Studies of the ectomycorrhizal symbiosis have highlighted the role of transcriptional regulation in controlling the morphological stages of symbiosis differentiation. To examine gene-activity changes associated with the development of the ectomycorrhizal symbiosis, we have performed expression profiling using poplar, eucalypt and Pisolithus cDNA arrays. A marked change in the gene expression in the mycobiont and the host-plants was observed at multiple levels: (a) a general activation of the protein synthesis machinery probably supporting an intense cell division/proliferation, (b) an increased accumulation of transcripts coding for cell wall proteins in hyphae and roots probably involved in the symbiotic interface formation, and (c) the upregulation of energy metabolism in colonised roots. This data suggests a highly dynamic environment in which symbionts are sending and receiving signals, are exposed to high levels of stress conditions and are remodeling their tissues. With multiple EST/cDNA array programmes dealing with ectomycorrhizal associations, we will have in a near future an unparalleled opportunity to ask which genetic features are responsible for common/divergent traits involved in this symbiosis. A few of the many possible breakthroughts will be in characterisation of common transcriptional and transduction networks and new insights into unique metabolic routes critical for mycorrhiza functioning.