In 1999, disease outbreaks in juvenile Atlantic cod Godus morhua that showed the classic signs of viral encephalopathy and retinopathy (VER) were reported in Nova Scotia. Brain and retinal tissues from moribund cod showed diffuse degenerative vacuolative encephalopathy and degenerative histiocytic retinitis. The affected bra-in and retinal tissues were observed to be positive for nodaviral antigens by means of immunohistochemical techniques. We partially characterized a nodavirus-like agent from brain and eye tissues and cell culture using reverse-transcriptase polymerase chain reaction and primer sets originally designed for amplification of white trevally Caranx dentex (also known as striped jack Pseudocaranx dentex) and Atlantic halibut Hippoglossus hippoglossus nervous necrosis virus coat (capsid) proteins. Sequencing of the T2 region of the coat protein revealed high similarities (>85% nucleotide identity) to the coat protein genes of other fish nodavirus strains, especially those of Atlantic halibut and barfin flounder Verasper moseri, which possessed 92% nucleotide identity. Based upon the sequence of its T4 region, this nodavirus is a member of the barfin flounder nervous necrosis virus clade. This is the first report of VER in Atlantic cod and the first report of this disease agent on the Atlantic coast of North America.