The presence of cyanobacterial toxins such as microcystin in drinking water supplies poses a serious health risk to humans and may result in chronic liver injury and possibly in the promotion of liver tumors. It is thus important to monitor cyanobacterial densities and toxin levels in water reservoirs and, in the event of a bloom, to remove these toxins by adequate water treatment procedures. Conventional water treatment is ineffective in reducing cyanobacterial toxin levels to below acutely toxic concentrations. Previous studies have suggested that the best method to remove cyanobacterial toxins from drinking water is oxidation with ozone. In order to investigate the efficacy of ozone in the removal of cyanobacterial toxins, Microcystis aeruginosa PCC 7806 and Oscillatoria rubescens from Lake Zurich, Switzerland were ozonated in a batch reactor with O3 concentrations ranging from 0,3-2 mg/l for 9 min contact time and 60 min reaction time (ozone off). The presence of toxins was detected by a protein phosphatase inhibition (PPI) assay, HPLC, ELISA, immunoblotting and a primary hepatocyte toxicity assay. Products of ozonation obtained following incomplete oxidation of microcystins were analyzed by HPLC, ELISA, PPI and immunoblotting. The results show that the residual toxicity of the cyanobacterial material depended on the cell density, the ozone concentration, the duration of ozonation and the temperature of the ozonated water. Complete detoxification of 105 cells/ml was achieved with 1.0 mg O3/l. Ozonation of higher cell densities resulted in increased toxicity due to lysis of cyanobacterial cells and release of toxins. A residual level of ozone (0,05 mg/l) should therefore remain in order to completely destroy the toxins. The importance of this was shown by the observation that ozonation products may display PPI and were detectable by ELISA and immunoblotting.