In this study, we carried out measurements of genotoxic organics, i.e. 11 kinds of polycyclic aromatic hydrocarbons (PAHs), 8 kinds of nitrated polycyclic aromatic hydrocarbons (NPAHs), and 3-nitrobenzanthrone (3-NBA), in diesel-engine exhaust particles (DEP) from combustion processes of biodiesel fuel (BDF) synthesized from vegetable oils, petroleum diesel fuel, and their mixtures. All PAHs and NPAHs in the DEP collected decreased with increasing the content of BDF in the fuel. The reduction rates of PAHs and NPAHs emitted from the diesel-engine by replacing the PDF to BDF were in the range from 44 to 89%. While the reduction rate of 3-NBA, which is one of the oxy-aromatic compounds, was lower than those of PAHs and NPAHs, it was only 20%. PAHs can be generated by the cyclization and/or polymerization of hydrocarbons, especially of aromatic hydrocarbons, when fuels incompletely burn. However, BDF containing 20 vol.% of benzene showed no increase of PAHs and NPAHs emission compared to the BDF without benzene through the fuel-combustion process. This fact indicates that the drastic reduction of PAHs and NPAHs by using BDF is not due to the content of aromatics in the fuel, but the high oxygen content in its molecular structures. The mutagenic activity of the soluble organic fraction of the DEP also remarkably decreased with increasing of the BDF contents in the fuel. It is apparent from the results that BDF is a quite effective alternative fuel to reduce the genotoxic potentials of DEP.