The by-caught harbour porpoises in commercial fisheries have raised concerns over their conservation status in the Baltic region. One important aspect for management purposes is porpoise movements within the region. We measured stable isotopes in cod, herring and hagfish, species that are important prey for harbour porpoises in the Baltic region. Bone collagen in fish from the marine Kattegat/Skagerrak was significantly enriched in 13C compared with collagen in fish from the brackish Baltic Sea. However, despite the isotopic variation seen in their prey, we found no difference in 13C in harbour porpoise collagen from the two areas. In fact, only eight of 24 porpoises had isotope signatures corresponding to those estimated for the diet in the area where they were caught. Our general conclusion is that porpoises move between the Baltic and Kattegat/Skagerrak Seas. Future studies are needed to evaluate the magnitude of these movements.