Pancreas disease (PD) is a viral disease of farmed salmonid fish, which causes huge economic losses. Pathological changes in skeletal muscle, pancreas and heart are hallmarks of PD. Stakeholders in the fish-smoking industry have claimed that fillets from PD-affected Atlantic salmon, Salmo salar L., are of poor quality. We therefore examined harvest-ready, clinically healthy Atlantic salmon from a population of fish previously affected by PD. Histopathological changes in skeletal muscle tissues ranged from minor to severe. Fillet quality measurements showed that fish with severe skeletal muscle changes provided a paler raw fillet and a yellowish and harder cold-smoked fillet than normal. PD had no significant effect on fillet gaping, bacteriological quality or off-odour development during storage. An unexpected finding was a significant subendocardial fibrosis in 23% of the PD-affected fish. The latter may indicate susceptibility to stress-related heart failure.