Little information exists on the toxicological hazards associated to organo-modified clays. We evaluated the cytotoxicity of a series of pristine and organo-modified nanoclays in different cell lines. The calculated IC50 values for cell viability ranged from 1.4 to 47 μg/mL for the six organoclays used and were above 100 μg/mL for the pristine nanoclays. The IC50 values of the organoclays were driven by the proportion and structure of the quaternary ammonium compound used as surface organic modifier. No differences in cell toxicity were observed between the large and small size (additional milling step) nanoclay batches, although their size differences related mostly to upper range of the size distribution. Despite their lower toxicity, pristine nanoclays induced apoptosis and were found in cytoplasmic vesicles of exposed cells. Organoclays were also found in cytoplasmic vesicles, although the size of the agglomerates was larger and the efficiency of uptake was considerably lower.