The occurrence of Gyrodactylus salaris in the River Tornionjoki was investigated in 2000-2004. Infection of salmon parr, Salmo salar, was common in the uppermost reach of the river system but decreased downstream and was rare in the lowermost reach. This pattern was consistent across the study period regardless of varying water temperatures. The oldest age groups of parr were more often infected than younger ones throughout the river system, irrespective of their origin (wild or stocked). Parasite-free hatchery-reared 1-year-old parr became infected during their first summer in the wild. Downmigrating salmon smolts had a high prevalence of infection, but their role in the distribution of infection seemed unimportant. On grayling, Thymallus thymallus, we observed only the grayling-specific clade of Gyrodactylus. We found no indication of grayling participating in the epidemiology of infection on salmon. The salmon parr and smolt population in the Tornionjoki has been at its height during the late 1990s and 2000s. Our results indicate that G. salaris infection in this Baltic river has no devastating effects on the salmon population as it has had in salmon rivers flowing into the North Atlantic and White Sea.