Among the new technologies developed for the heavy-duty fleet, the use of Selective Catalytic Reduction (SCR) aftertreatment system in standard Diesel engines associated with biodiesel/diesel mixtures is an alternative in use to control the legislated pollutants emission. Nevertheless, there is an absence of knowledge about the synergic behaviour of these devices and biodiesel blends regarding the emissions of unregulated substances as the Polycyclic Aromatic Hydrocarbons (PAHs) and Nitro-PAHs, both recognized for their carcinogenic and mutagenic effects on humans. Therefore, the goal of this study is the quantification of PAHs and Nitro-PAHs present to total particulate matter (PM) emitted from the Euro V engine fuelled with ultra-low sulphur diesel and soybean biodiesel in different percentages, B5 and B20. PM sampling was performed using a Euro V - SCR engine operating in European Stationary Cycle (ESC). The PAHs and Nitro-PAHs were extracted from PM using an Accelerated Solvent Extractor and quantified by GC-MS. The results indicated that the use of SCR and the largest fraction of biodiesel studied may suppress the emission of total PAHs. The Toxic Equivalent (TEQ) was lower when using 20% biodiesel, in comparison with 5% biodiesel on the SCR system, reaffirming the low toxicity emission using higher percentage biodiesel. The data also reveal that use of SCR, on its own, suppress the Nitro-PAHs compounds. In general, the use of larger fractions of biodiesel (B20) coupled with the SCR aftertreatment showed the lowest PAHs and Nitro-PAHs emissions, meaning lower toxicity and, consequently, a potential lower risk to human health. From the emission point of view, the results of this work also demonstrated the viability of the Biodiesel programs, in combination with the SCR systems, which does not require any engine adaptation and is an economical alternative for the countries (Brazil, China, Russia, India) that have not adopted Euro VI emission standards.