The extensive applications of nanoparticle materials in biomedical and biotechnological fields trigger the rapid development of nanotoxicology, because nanoparticles are reported to cause more damage than larger ones when human exposure to them. In the present manuscript, we prepared a series of zeolite nanocrystals with different frameworks, sizes, compositions and shapes, and provided the first report on their toxic difference. As our results, the toxicities of zeolite nanoparticles depend on their size, composition and shape when they are exposed to HeLa cells. The pure-silica nanozeolite silicalite-1 displays nontoxicity, but aluminum-containing nanozeolites, such as ZSM-5, LTL, and LTA, show a dose-dependent toxic manner. The different shapes of nanozeolites can lead to different cytotoxicities, while the influences of the surface charge differences of various nanozeolites on their toxicities are unconspicuous. More importantly, caspase-3 activity and LDH released assays showed that the toxic nanozeolites seem to induce cell necrosis rather than cell apoptosis by the damnification for the cell membranes. These results are expected to direct the applications of nanozeolites with different structures and shapes in biomedicine and clinic science. (C) 2011, The Society for Biotechnology. Japan. All rights reserved.