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Context: Soy biodiesel is the predominant biodiesel in the USA, but there is little understanding of the classes of chemicals responsible for the mutagenicity of its emissions.Objective: We determined some of the chemical classes responsible for the mutagenicity of the particulate matter (PM) of the emissions from petroleum diesel (B0) and biodiesel containing increasing concentrations of soy methyl esters (B20, B50, and B100).Materials and methods: We subjected organic extracts of the PM to bioassay-directed fractionation by sequential elution on silica gel with solvents of increasing polarity to produce four fractions per fuel. We injected these onto high performance liquid chromatography to produce 62 sub-fractions per fraction based on chemical polarity and evaluated all fractions and sub-fractions for mutagenicity in Salmonella. We correlated the results with the concentrations of 32 polycyclic aromatic hydrocarbons (PAHs) in the fractions.Results: The mutagenicity-emission factors of the fractions generally decreased with increasing concentrations of soy in the fuel. Despite the different chemical compositions of the fuels, the extractable organics of all four emissions had similar features: approximate to 60% of the mass was nonpolar, non-mutagenic compounds; most of the PAHs were polar; and most of the mutagenicity was due to weakly polar and polar compounds. Some of the mutagenicity of B20 was due to highly polar compounds.Conclusions: The PM from soy biodiesel emissions was less mutagenic than that from petroleum diesel, and this reduction was associated with reduced concentrations of various weakly polar, polar, and highly polar mutagens, including PAHs, aromatic amines, nitroarenes, and oxy-PAHs.