The prevalence of Clostridium botulinum type E gene in fish and fishery products of commercial importance in Finland was determined using a quantitative PCR analysis. The contamination level in 438 raw fish samples from intestines, surface and whole fish and 208 fish roe samples varied from 10–40% and from 4–14% respectively, depending on the fish species studied. The presence of C. botulinum in European wild freshwater fish and roe was demonstrated for the first time by isolation of the organism from PCR-positive samples. Five percent of 214 vacuum-packed and 3% of 123 air-packed fishery product samples examined at retail level were positive for the botulinum neurotoxin type E gene. A contamination level of 10% in vacuum-packed hot-smoked whitefish was detected. The results demonstrate that C. botulinum type E poses a serious health risk for those consuming fishery products from the Baltic Sea area.