Infectious pancreatic necrosis virus (IPNV), a member of the genus Aquabirnavirus and family Birnaviridae, is an unenveloped icosahedral virus with two segments of double-stranded RNA. IPNV causes acute infection in salmonid fry and fingerlings with high mortality. However, this mortality is low as the age increases and survivors become IPNV-carrier fish. In this study, IPNV persistent infection was established in rainbow trout with no clinical signs or mortality. TUNEL staining and immunohistochemistry showed that IPNV antigen-positive cells did not have an apoptotic nucleus in almost all tissue sections and leucocyte smears, indicating that apoptosis was not induced in IPNV antigen-positive cells. The IPNV genome detected by in situ RT-PCR was more frequent than detection of the IPNV antigen by immunohistochemistry in the kidney, spleen, and liver. This result implies that the successive replication would not occur in many IPNV-infected cells. Further, apoptotic cells were predominant in the tissue sections where the signal-positive cells were frequently detected. Therefore, the presence of apoptosis in this study might be associated with host defense mechanisms, which eliminates IPNV-infected cells by the recognition of IPNV genome at the early stage of infection.