Microcystins (MCs) are toxins of heptapeptidic structure produced by toxic cyanobacteria in surface eutrophic waters. MCs are known to be hepatotoxic in humans, but they are also able to induce gastrointestinal alterations, allergic reactions, irritation, and pneumonia-like symptoms. The impact of MC-LR, one of the most common cyanobacterial toxins, was studied on the Caco-2 cell line, a commonly used enterocytic model, established from a human colon carcinoma. Caco-2 cells were differentiated in order to compare the effect of MC-LR in differentiated and non-differentiated cells. They were seeded in a 96-well microtiter plate and treated with MC-LR pure standard (98% purity). The effects of different concentrations of this cyanotoxin (50, 100, 150, and 200 microM) were investigated at 24 and 48 h of exposure by morphological observation and biochemical changes (total protein content, neutral red uptake, and MTS metabolization). Differentiated Caco-2 cells were slightly more sensitive than undifferentiated cells. Moreover, toxic effects induced by MCs were higher at 48 h compared to those observed at 24 h. The most sensitive endpoint for the cell line was the reduction of total protein content. Morphological changes induced by MC-LR were reduction in the cell number and hydropic degeneration, being these alterations more evident 48 h after the exposure to MC-LR.