The mutagenic activity of size-fractionated atmospheric particulate matter (PM) was investigated at both a roadside site and a suburban site in Saitama, Japan. Sampling was carried out using a low-pressure cascade impactor between January and February 2005. The mutagenic activity of the size-fractionated PM was determined by the Ames test using Salmonella typhimurium strain TA98 without metabolic activation (S9). Most of the mutagenic activity was found in the fine particle fraction (< 2.1 μm) at both sites. There was almost no difference in the contribution of fine particles to the mutagenic activity of total PM between the two sites. On the other hand, there was a clear difference in the contribution of ultrafine particles (< 0.12 μm) to the mutagenic activity between the two sites. At the suburban site, ultrafine particles accounted for 5.7% of the mutagenic activity of total PM. In contrast, at the roadside site, ultrafine particles contributed as much as 12% to the mutagenic activity of total PM, although their contribution to the total PM mass was only 2.3%. Moreover, the mutagenic activity per unit air volume in the ultrafine particle fraction at the roadside site (1.2 revertants/m³) was 3.1-fold higher than that at the suburban site (0.38 revertants/m³), although the activity in the fine particle fraction at the roadside site was only 1.4-fold higher than that at the suburban site. These results indicated that, with regard to mutagenicity, the health risk due to ultrafine particles is relatively high at roadside areas.