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Rapeseed oil methyl ester, two common fuels and one artificial blend were investigated their effects on particulate emissions. A heavy-duty diesel engine equipped with a diesel oxidation catalyst (DOC) was used for this test. Properties such as composition of particulate matter, as well as particle size and number distributions were measured using an electronic low pressure impactor (ELPI) and a scanning mobility particle sizer (SMPS) besides the regulated emissions: carbon monoxide (CO), hydrocarbons (HC), nitrogen oxides (NOx), and particulate matter (PM). Furthermore investigations were carried out regarding the influence of dilution temperature on particle number distribution measured via SMPS. Studies were carried out with and without a DOC. Additionally the mutagenic potency of the particulate and gaseous emissions was determined using the Ames test. RME led to lower regulated emissions than common diesel fuel with exception of NOx.