This study evaluated the concentration profiles of regulated and unregulated pollutants emitted from a stationary diesel engine cycle, operating at the speed of 1800 rpm and 0% load, using biofuels and binary blends. The experimental test considered fuel burning time on three different periods and storage times. The operation of the engine when it is still cold, for example at 15 minutes, showed negative effect on particulate matter (PM), benzene and ethylbenzene emissions in pure soybean biodiesel (B100) compared to the blend of diesel with 5% biodiesel (B5). Regarding to the concentration of mono aromatics, aliphatic hydrocarbons and polycyclic aromatic hydrocarbons (PAH), this study showed similar results to those reported in the literature, where B5 fuel emits more pollutants than pure biodiesel. However, comparing some pollutants individually, benzene and ethylbenzene emissions were higher for B100 and pure soybean biodiesel with butil-hydroxyanisol additive (B100 Adt). The B5 showed the highest concentration profile for the PAH sum in the gaseous and particulate phases in longer engine operation periods.