Efforts are under way to reduce diesel engine emissions (DEE) and their content of carcinogenic and mutagenic polycyclic aromatic hydrocarbons (PAH). Previously, we observed reduced PAH emissions and DEE mutagenicity caused by reformulated or newly developed fuels. The use of rapeseed oil as diesel engine fuel is growing in German transportation businesses and agriculture. We now compared the mutagenic effects of DEE from rapeseed oil (RSO), rapeseed methyl ester (RME, biodiesel), natural gas-derived synthetic fuel (gas-to-liquid, GTL), and a reference petrodiesel fuel (DF) generated by a heavy-duty truck diesel engine using the European Stationary Cycle. Mutagenicity of the particle extracts and the condensates was tested using the Salmonella typhimurium mammalian microsome assay with strains TA98 and TA100. The RSO particle extracts increased the mutagenic effects by factors of 9.7 up to 17 in strain TA98 and of 5.4 up to 6.4 in strain TA100 compared with the reference DF. The RSO condensates caused up to three times stronger mutagenicity than the reference fuel. RME extracts had a moderate but significantly higher mutagenic response in assays of TA98 with metabolic activation and TA100 without metabolic activation. GTL samples did not differ significantly from DF. Regulated emissions (hydrocarbons, carbon monoxide, nitrogen oxides (NO.), and particulate matter) remained below the limits except for an increase in NO, exhaust emissions of up to 15% from the tested biofuels. Published by Elsevier Ltd.