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Thiaminase activity was determined for Gulf of Bothnia (GB) and Gulf of Finland (GF) Baltic herring Clupea harengus membras, sprat Sprattus sprattus and three-spined stickleback Gasterosteus aculeatus sampled from either trawl or gillnet catches or from Baltic salmon Salmo salar stomachs. The thiaminase activity in Baltic herring was about 10-fold higher than that in sprat, and there was almost no thiaminase activity in three-spined stickleback. Thiaminase activity of undigested Baltic herring found in Baltic salmon stomachs was significantly higher than that of trawl-caught Baltic herring from the same sea area, suggesting that there may be a higher risk of predation for Baltic herring with high thiaminase activity, possibly linked to their health. Thiaminase activity of the gastrointestinal contents of Baltic salmon, feeding almost entirely on Baltic herring in the GB, was significantly higher than for Baltic salmon feeding on both Baltic herring and sprat in the GF. Therefore, Baltic herring may be the major source of thiaminase for Baltic salmon. A tank experiment demonstrated that thiaminase activity in Baltic herring may vary, even within very short time periods. The results were consistent with the hypothesis that the thiaminase content in Baltic salmon forage fish may be an important link in the aetiology of the thiamine deficiency syndrome, M74, in Baltic salmon.