During the last two decades, more than 100 cattle deaths have been reported from 11 alpine sites in south-eastern Switzerland. Pathological findings and the histological examination of their organs strongly indicated acute hepatotoxicosis. Clinical symptoms suggestive of neurotoxicity were also observed in some cases. To elucidate the etiology of these poisonings, different water bodies in one of the affected alpine pastures were investigated for cyanobacterial toxins. The waters were highly oligotrophic, cold and turbid, and the ice-free period was limited to 3–4 months. The algal community in these waters consisted mostly of benthic cyanobacteria forming dense mats on the surface of sediments and on submerged rocks. Oscillatoria limosa and Phormidium konstantinosum (=Oscillatoria tenuis) dominated these populations, but occasionally other species of Oscillatoria, Phormidium, Tychonema and Pseudanabaena also occurred in the mats. Samples from the cyanobacterial mats yielded positive results in a protein phosphatase inhibition assay, reacted with antibodies against microcystins in an enzyme-linked immunosorbent assay and were hepatotoxic in a mouse bioassay. The same cyanobacterial material also included neurological effects in mice. High-performance liquid chromatography was used to identify a microcystin, in these cyanobacterial samples as well as in the corresponding lake water. To our knowledge, this is the first documented example of hepatotoxicity associated with benthic cyanobacteria, and the first report of toxic cyanobacteria from the remote, oligotrophic alpine environment.