Infectious salmon anaemia virus (ISAV), an economically important pathogen for the salmon farming industry in the northern hemisphere, closely resembles orthomyxoviruses, which include the influenza viruses. The influenza viruses are characterized by their continuous change in genetic material driven by the hosts immune defence, and as a consequence, a great variation in the severity of the infection is seen. In ISAV infections, differences in the course of the disease and clinical signs have been observed, as well as in cell culture replication. These differences indicate variations both in the virulence and antigenic composition of the virus. Nucleotide and amino acid sequence alignments were performed on 33 ISA disease outbreaks picked from all along the Norwegian coast covering a ten year period. A polymorf region was detected, and depending on type of variation the disease outbreaks fell into eight separate groups. From some of the more diffuse disease outbreaks, where one had not been able to isolate virus, cloning of RT-PCR products from diseased fish homogenates resulted in detection of not just one, but two to three variable groups from the same outbreak. Comparisons between members of the groups with regard to development of cytopathogenic effect and virus titres in cell culture showed variation between the groups. Here we describe the ISAV hemagglutinin gene: both nucleotide / amino acid comparisons and the estimated 3D structure of this molecule.