In euryhaline teleosts, osmoregulation is a fundamental and dynamic process that is essential for the maintenance of ion and water balance, especially when fish migrate between fresh water (FW) and sea water (SW) environments. The European eel has proved to be an excellent model species to study the molecular and physiological adaptations associated with this osmoregulatory plasticity. The life cycle of the European eel includes two migratory periods, the second being the migration of FW eels back to the Sargasso Sea for reproduction. Various anatomical and physiological changes allow the successful transition to SW. The aim of this study was to use a microarray approach to screen the osmoregulatory tissues of the eel for changes in gene expression following acclimation to SW. Tissues were sampled from fish at selected intervals over a 5 month period following FW/SW transfer and RNA was isolated. Suppressive subtractive hybridisation (SSH) was used for enrichment of differentially expressed genes. Microarrays comprising 6144 cDNAs from brain, gill, intestine and kidney libraries were hybridised with appropriate targets and analysed; 229 differentially expressed clones with unique sequences were identified. These clones represented the sequences for 95 known genes, with the remaining sequences (59 %) being unknown. The results of the microarray analysis were validated by quantification of 28 differentially expressed genes by Northern blotting. A number of the differentially expressed genes were already known to be involved in osmoregulation but the functional roles of many others, not normally associated with ion or water transport, remain to be characterised.