The aim of this study was to evaluate the deposition in the respiratory tract of nanoparticles (11.5nm to 365.2nm) from the burning of diesel, biodiesel and additives. The studied fuels were pure diesel (D), binary mixture of pure diesel with 11% biodiesel (B11) and ternary mixture of pure diesel, with 11% biodiesel and with the biocatalyst Xmile (B11X). The impact of nanoparticles on health was assessed using the MPPD lung model. From the tests, the burning of the studied fuels showed concentration of number of particles in the accumulation mode (50nm to 120 nm). When comparing fuels, it was clear that B11 emits more particles and has a greater deposition capacity in the lung. B11X has been shown to be efficient in reducing pollutant emissions as well as impacting human health.