The aim of the paper is the comparison of the injection process with two fuels, a standard diesel fuel and a pure biodiesel, methyl ester of soybean oil. Multiphase cavitating flows inside injector nozzles are calculated by means of unsteady CFD simulations on moving grids from needle opening to closure, using an Eulerian-Eulerian two-fluid approach which takes into account bubble dynamics. Afterward, spray evolutions are also evaluated in a Lagrangian framework using results of the first computing step, mapped onto the hole exit area, for the initialization of the primary breakup model. Two nozzles with cylindrical and conical holes are studied and their behaviors are discussed in relation to fuel properties. Nozzle flow simulations highlighted that the extent of cavitation regions is not much affected by the fuel type, whereas it is strongly dependent on the nozzle shape. Biodiesel provides a slightly higher mass flow in highly cavitating nozzles. On the contrary using hole shaped nozzles (to reduce cavitation) diesel provides similar or slightly higher mass flow. Comparing the two fuels, the effects of different viscosities and densities play main role which explains these behaviors. Simulations of the spray evolution are also discussed highlighting the differences between the use of fossil and biodiesel fuels in terms of spray penetration, atomization and cone-angle. Usage of diesel fuel in the conical convergent nozzle gives higher liquid penetration. (C) 2011 Elsevier Ltd. All rights reserved.