Viral infections in fish are common in both natural and cultured fish populations and the spread of infectious disease is a serious threat to both natural ecosystems and commercial exploitations. A significant body of studies have addressed the host response to viral infection including the efficacy of DNA vaccines however we still have a fragmented vision of both pathologies associated with viral infection and the immune response to those across fish species. Many studies have concentrated upon freshwater fish including the zebrafish (Danio rerio) and the Rainbow trout (Oncorhynchus mykiss) whereas the majority of marine fish studies address the Atlantic salmon (Salmo salar). Here we provide a comprehensive review concentrating upon the salient pathological features of the most common viral infections including examples of the Betanodaviruses, Birnaviruses, Rhabdoviruses and the Isavirus in cultured fish with emphasis where possible upon non-salmonid cold water adapted marine species. In parallel we review the current state of the art mainly in reference to gene expression studies describing the host innate immune response concentrating upon the inflammatory response and its relationship toward anti-viral immunity in fish. Due to the complexity of the observed responses and the limitations of candidate gene expression studies to describe global biological processes, recent efforts in the use of microarray analysis for the study of the anti-viral response have been highlighted including members of the Pleuronectiform and the Perciform families. Finally we review the potential of the zebrafish to become a significant biological model in the elucidation of the molecular mechanisms underlying the piscine immune response to viral infection. © 2010 Bentham Science Publishers Ltd.