A reverse transcription polymerase chain reaction (RT-PCR) was used to study the early phase of infectious salmon anaemia virus (ISAV) infection in Atlantic salmon Salmo salar L. The detection threshold for the RT-PCR was estimated to be 0.01 to 0.1 TCID50. A protocol that closely mimics the conditions in populations of farmed salmon was used. The major port of ISAV entry was most likely the gills, but oral entry could not be excluded. The gills and heart were RT-PCR positive 5 d post infection and there was a rapid viraemic spread of the virus after entry. Ten or more days post infection, most organs yielded RT-PCR positive samples. The viral load of the fish followed a 2-phase curve with the first maximum at approximately 15 d and a minimum around 25 d. After 25 d, there was a steady increase in viral load until all sampled organs eventually became positive. In an experiment in which the transportation of material from field to diagnostic laboratory was simulated, the transportation of whole fish was found to be optimal for the performance of RT-PCR.