Microcystin-LR (MC-LR) is the main isoform of hepatotoxin produced by cyanobacteria, which occur worldwide in the aquatic environment. The present study investigated the in vitro toxic MC-LR effects on immune cells isolated from the blood of carp. Cells were exposed to different MC-LR concentrations ranging from 0.01 to 1 µg ml–1 for 2, 6 and 24 h. In addition, the effect of the toxin on the phagocytic activity of leukocytes and on actin and tubulin re-organization in phagocytic cells was studied. We observed that MC-LR induces apoptosis in lymphocytes 2 h after incubation, whereas high toxin concentrations induced necrosis in lymphocytes in a time- and concentration-dependent manner. Incubation of the cells for 2 h with 0.1 and 1 µg ml–1 MC-LR inhibited phagocytosis without affecting apoptosis or glutathione (GSH) levels. Moreover, at this time point and with these concentrations, the toxin also induced a significant re-organization of the actin cytoskeleton in phagocytes, which subsequently collapsed around the nucleus leading to cell shrinkage and the disappearance of filopodia. These results suggest that both phagocytes and lymphocytes are targets for MC-LR and the disturbances of phagocytosis may impair the balance of the immune system. Copyright © 2012 John Wiley & Sons, Ltd.