Salmon B-cells and neutrophils were studied by flow cytometry in IPNV infected salmon. A highly virulent strain of IPNV was used for challenge of parr and post-smolts. The parr were challenged by intraperitoneal (ip) injection while salmon post-smolts were challenged by ip injection or cohabitation. No mortality occurred in the parr groups, but a cumulative mortality of about 50% was obtained in cohabitant infected post-smolt groups and less than 10% in ip challenged post-smolts. The virus levels were low in head kidney (HK) samples from survivors compared to dead fish. The percentages of neutrophilic granulocytes and Ig+ cells (B-cells) were analysed using HK and blood samples from survivors. The cell populations were identified by monoclonal antibodies (MAb) E3D9, recognising neutrophils, and G2H3 recognising Ig+ cells (B-cells). Parr sampling for leucocyte analyses took place about 1.5 weeks prior to and about 4 weeks post challenge. This corresponded to about 8 and 2.5 weeks before the fish were adapted to seawater transfer. In parr head kidney leucocytes (HKL) we observed significantly lower (p < 0.05) levels of neutrophils in ip infected fish compared to non-infected control fish. The post-smolt sampling from infected fish took place 2 weeks prior to and in the fifth and sixth week post challenge. HKL samples from both surviving cohabitants and ip injected fish had significantly (p < 0.05) lower levels of neutrophils than non-infected control fish. The cohabitant fish also had significantly (p < 0.05) higher levels of B-cells in HKL compared to ip injected fish. No significant changes in B-cells in HKL or peripheral blood leucocytes (PBL) was observed in infected parr or ip infected post-smolts compared to control fish. The relative leucocyte levels of the fish prior to challenge and in non-infected control fish are in accordance with earlier findings. The results indicate that non-specific immune cells like neutrophils are highly influenced by IPNV infection of parr and post-smolts several weeks post challenge.