Microcystins (MC) are a group of amphiphatic peptide hepatotoxins and protein phosphatase inhibitors produced by certain cyanobacteria (blue-green algae). Microcystins are believed to require an active transport mechanism to penetrate the plasma membranes of animal cells. In this study the surface barostat technique showed that two more hydrophobic microcystins MC-LF, containing Leu and Phe, and MC-LW, containing Leu and Trp, had a higher surface activity on an egg phosphatidylcholine-cholesterol (7:3, molar ratio) monolayer as compared to that of a more hydrophilic variant MC-LR, containing Leu and Arg. Fluorescence anisotropy measurements of 1-[4-(trimethylamine)phenyl]-hexa-1,3,5-trien (TMA-DPH) were used to assess changes in the fluidity or lipid packing of model membranes in the presence of toxins. All three toxins caused a decrease in the steady-state anisotropy of TMA-DPH, suggesting that the toxins interacted with the membranes. The change in anisotropy was more pronounced for MC-LF and MC-LW than for MC-LR. Moreover, the fluorescence emission maximum of Trp in MC-LW was shifted slightly towards a shorter wavelength and the intensity was enhanced when allowed to interact with lipid vesicles, suggesting that the single Trp in MC-LW moved into a more unpolar environment when interacting with the vesicles. The differences between hydrophilic and hydrophobic microcystins could result in changes in organotropism, toxicokinetics and bioaccumulation.