Infectious salmon anemia virus (ISAV) is the causative agent of an important viral disease threatening the Atlantic salmon aquaculture in Norway and many other countries. Although its structure and pathogenesis is well described little is known about its effects on the expression of genes related to apoptosis in the host cell. Apoptosis is a genetically controlled process of cell suicide in response to a variety of stimuli and is considered a part of the innate immune response to virus infection, limiting the time and cellular machinery available for viral replication. Previous studies have shown that several RNA viruses induce apoptosis in host-cells. A recent study also suggests that the CPE observed in ISAV-infected SHK-1 and CHSE-214 cells is associated with apoptosis.Studies of ISAV-induced apoptosis may provide a clearer picture of the cellular mechanisms of viral persistence and pathogenesis in ISAV infection. In the present study we wanted to investigate the effect of ISAV infection on the expression of apoptosis related genes in Atlantic Salmon (Salmo salar L.) cells. By using a quantitative real-time PCR approach we analyzed the regulation of key apoptosis related genes during early stages of ISAV infection in vitro. Two different permissive cell lines for ISAV were used, Atlantic salmon head kidney (ASK) cells and salmon head kidney (SHK-1) cells. Our results strongly indicates that IFN-α, Mx and cIAP-1 are up regulated during ISAV infection in both ASK and SHK-1 cell lines. We also showed that viral mRNA increased steadily throughout the infection, in spite of the increased levels of IFN-α and Mx, indicating that these genes have little or no antiviral effect on ISAV in Atlantic salmon cells.