Background: Muscle fibre hyperplasia stops in most fish when they reach approximately 50 % of their maximumbody length. However, new small-diameter muscle fibres can be produced de novo in aged fish after muscle injury.Given that virtually nothing is known regarding the transcriptional mechanisms that regulate regenerativemyogenesis in adult fish, we explored the temporal changes in gene expression during trout muscle regenerationfollowing mechanical crushing. Then, we compared the gene transcription profiles of regenerating muscle with thepreviously reported gene expression signature associated with muscle fibre hyperplasia.Results: Using an Agilent-based microarray platform we conducted a time-course analysis of transcript expressionin 29 month-old trout muscle before injury (time 0) and at the site of injury 1, 8, 16 and 30 days after lesions weremade. We identified more than 7000 unique differentially expressed transcripts that segregated into four majorclusters with distinct temporal profiles and functional categories. Functional categories related to response towounding, response to oxidative stress, inflammatory processes and angiogenesis were inferred from the early upregulatedgenes, while functions related to cell proliferation, extracellular matrix remodelling, muscle developmentand myofibrillogenesis were inferred from genes up-regulated 30 days post-lesion, when new small myofibres werevisible at the site of injury. Remarkably, a large set of genes previously reported to be up-regulated in hyperplasticmuscle growth areas was also found to be overexpressed at 30 days post-lesion, indicating that many features ofthe transcriptional program underlying muscle hyperplasia are reactivated when new myofibres are transientlyproduced during fish muscle regeneration.Conclusion: The results of the present study demonstrate a coordinated expression of functionally related genesduring muscle regeneration in fish. Furthermore, this study generated a useful list of novel genes associated withmuscle regeneration that will allow further investigations on the genes, pathways or biological processes involvedin muscle growth and regeneration in vertebrates.