The characterisation of 2 infectious salmon anemia virus (ISAV) proteins is described. Proteins were harvested from ISAV-infected Chinook salmon embryo (CHSE)-214 cell culture by continuous elution denaturing gel electrophoresis, enabling the harvest of specific molecular weight fractions. Through the use of a polyclonal antiserum to ISAV, it was possible to identify a potentially autolytic major antigen of 72 kDa and a glycosylated protein of approximately 38 kDa which varied in size depending on cell line compatibility. N-terminal amino acid sequencing of the glycosylated proteins suggests that it is encoded by segment 6 of the ISAV genome. Further, sequence analysis of the glycosylated protein account for the variable molecular weight and may explain differences in host cell compatibility.