We have studied the effect of chemical composition of biodiesel fuel on the physical (volatility) and chemical (reactive oxygenated species concentration) properties of nano particles emitted from a modern common-rail diesel engine. Particle emissions from the combustion of four biodiesels with controlled chemical compositions and different varying unsaturation degrees and carbon-chain lengths, together with a commercial diesel, were tested and compared in terms of volatility of particles and the amount of reactive oxygenated species carried by particles. Different blends of biodiesel and petro diesel were tested at several engine loads and speeds. We have observed that more saturated fuels with shorter carbon chain lengths result in lower particle mass but produce particles that are more volatile and also have higher levels of Reactive Oxygen Species. This highlights the importance of taking into account metrics that are relevant from the health effects point of view when assessing emissions from new fuel types.