The complexity and large variability of transport-emitted aerosols leads to necessity of comprehensive characterization of their physico-chemical and toxicological properties, remaining great uncertainties in health effect assessments. Particles produced by combustion of fossil diesel (B0), 20% rapeseed methyl ester in fossil diesel (B20), and pure rapeseed methyl ester (B100) were sampled from exhaust of an Opel Astra diesel engine using sulfated ash, phosphorous and sulfur (SAPS) lube oil with low and high ash content. Microscopic and chemical characterization is performed to quantify the common and specific properties of diesel/biodiesel exhausts. Hydrophobic saturated aliphatic dominate diesel particle chemistry. Oxygen and nitrogen-containing functionalities are specific for more hydrophilic biodiesel particles. A full range of chemical species for individual particles is grouped by clustering technique combined with water-soluble ion measurements. Analysis of group abundance shows carbonaceous particles (soot externally mixed with inorganic salts) and inorganic fly ash (metal oxides) in a structure of exhaust, in correlation with inorganic contaminations in fuel and lube oil. Quantification of particle types in terms of physicochemical relevance supports the identification of groups which may act as biomicromarkers discriminating between diesel and biofuel exhaust and micromarkers of using high ash lube oil, thus providing a basis for correlative toxicological assessment of diesel/biofuel engine emissions.