To evaluate the role of particle size in cytotoxicity tests of nanomaterials (NMs), we exposed Chinese hamster cells to polystyrene (PS) spheres with defined diameters ranging from 0.1 to 9.2 μm. We found that the 4.45-μm PS particles were most cytotoxic while sizes 0.1 and 0.2 μm showed no cytotoxicity up to 1000 μg/ml. In the chromosome aberration test, the 4.45-μm PS particles induced polyploidy in a mass concentration-dependent manner in 24- and 48-h treatments. The 5.26-μm PS particles induced polyploidy only at 1000 μg/ml for 48 h. Next, we performed the cytotoxicity test with as-grown single walled carbon nanohorns (NHas). These were suspended in DMSO and then transferred into the culture medium followed by sonication. Six suspensions differently sonicated showed the same apparent toxicity, although the total particle size distributions differed. However, the sizes of NHas particles predicted to be most toxic from the experiments with PS particles, i.e. 1.01–4.47 μm constituted 40–60% of all particles in all six suspensions. The results suggest that the cytotoxicity of NMs in suspension depends on specific sizes of aggregates and therefore suspensions should be checked with regard to particle size distributions in assays of toxic effects. The uptake of particles into cells was confirmed by confocal microscopy.