The expression in kidney tissue of interferon type I (IFN gamma) and type II (IFN gamma) genes and two of their inducible genes, Mx and gamma IP were monitored, using qRT-PCR, in a population of Atlantic salmon prior to and over the period of smolting and sea water transfer. The smolting process was induced by photoperiod manipulation in October and smolts were transferred to sea water in December. Prior to extending the light period in October, the fish showed extremely low level expression of the genes assayed. However, immediately on extending the light and up until 1 week after transfer to sea water, 26 of the 90 fish sampled showed up-regulated expression for IFN alpha, Mx and gamma IP. The highest levels were shown by two fish on the 2 days prior to sea water transfer. Eleven fish displayed elevated expression of IFN gamma but there was no apparent association with smolting or sea water transfer or expression of the other genes. At the end of the sampling period, 30 fish were tested by standard virological methods and found to be virus free. The results indicate that during the smelting process, Atlantic salmon consititutively express IFN alpha and Mx mRNA. Those individuals which express Mx close to the time of transfer to sea water would be expected to have high levels of the anti-viral Mx protein in tissues for the longest time after sea water transfer. This could provide an innate defence against viral pathogens which post-smolts may encounter for the first time on entering the marine environment. Those individuals which express Mx early in the smolting process may be more at risk of developing IPN or other viral diseases as post-smolts. (c) 2006 Published by Elsevier Ltd.