Regulated gene expression is an important mechanism for controlling ectomycorrhizal symbiosis development. Our research programme is aimed to elucidate the coordination between development of mycorrhiza and the differential gene expression in both partners. We analyzed RNA levels from sequential samples of symbiotic tissues of Eucalyptus globulus bicostata or Populus tremula x alba, and the basidiomycete Pisolithus microcarpus progressing through ectomycorrhiza development using cDNA arrays. We derived groups of coordinately expressed genes using hierarchical and non hierarchical clustering algorithms. Major temporal patterns of induction/repression were observed with distinct groups of early-, middle-, and latetranscriptionally responsive genes to symbiosis formation. At earliest stages, the differentially expressed fungal genes included cell wall symbiosis-regulated proteins, hydrophobins and mannoproteins, whereas transcripts coding for defense-related proteins were up-regulated in plant tissues. Middle- and late-transcriptionally responsive genes coded enzymes of glycolysis, tricarboxylic acid cycle and amino acid biosynthesis, as well as protein synthesis, auxin metabolism and signal transduction components. These investigations showed that changes in morphology associated with mycorrhizal development were accompanied by changes in transcript patterns, but no ectomycorrhiza-specific genes were detected. Further studies are now needed to (1) identify signalling molecules cordinating these processes and (2) investigate the expression of the regulated genes in environmental samples.