Viral nervous necrosis (VNN) caused by beta-nodavirus affects many species of farmed marine fish, in particular juveniles. Apparently healthy, normally feeding, adult farmed Atlantic cod, Gadus morhua, were sampled in a farm 14 months after an outbreak of VNN with clinical signs. Following necropsy, brain and eye tissues were examined by histology, immunohistochemistry and polymerase chain reaction (PCR). Nodavirus-provoked cell death and inflammation was detected in eye and brain, particularly in the retina and cerebellum and differed from that previously described in Atlantic cod during clinical stages of VNN. Virus was detected both by PCR and immunohistochemistry. This is, to the best of our knowledge, the first description of pathological changes associated with chronic subclinical nodavirus infection in Atlantic cod. Our observations suggest that severe infection and pathological changes may go undetected if investigations are restricted to clinical examination and macroscopic evaluation at necropsy.