This work explores the effect of Fatty Acid Methyl Ester (FAME) as bio fuel on the particulate emission of a Diesel engine. The experiments were performed with various fuel combinations such as FAME, FAME/Diesel blends, and water/FAME/Diesel emulsions, which were directly injected into the combustion chamber of a Diesel engine. The analysis of the soot aggregates collected by thermophoresis on carbon grids using Transmission Electron Microscopy (TEM) gives information about the morphology of the particles. The Bosch number for the Diesel soot was measured with a smoke number detector, which uses the light reflection method. The fraction of volatile and non-volatile components was determined with a Thermal-Gravimetric Analyzer TGA. The particle number and their mobility sizes were measured with a Differential Mobility Particle Sizer (DMPS) system. The experiments show that FAME combustion leads to a significant reduction of the particle matter compared to Diesel combustion.