Fire is one of the most probable hazards of internal aggression in a nuclear facility. For many years, IRSN is conducting research programs dealing with the impact of a fire on the behaviour of containment devices of radioactive materials such as High Efficiency Particulate Air (HEPA) filters. It has been already observed, in addition to the well-known regimes of in depth and surface filtration, that for a high deposited mass of nanometrics aerosols (mainly soot particles emitted in case of fire) and low filtration velocity, an additional pressure drop increase occurs for pleated HEPA filters used in the French nuclear industry (Mocho and Ouf 2011). Up to now, little information is available in the literature about this last regime of filtration. The most probable phenomenon is an unbalance in the aerosol repartition along the pleat which causes a reduction of the filtration surface (Del Fabbro et al., 2002). This paper deals with an experimental method to measure the repartition of deposited nanoparticles in the depth of a pleat using embedded samples and electronic microscopy. In this study, HEPA filters were clogged at various controlled filtration velocities on a test bench generating nanoparticles aggregates of Zinc/Aluminium denoting similarities in terms of size and morphology to soot particles emitted in case of fire (Mocho et al., 2011). A pleat of 20 mm in depth of the pleated filter was stabilized in a polymer resin (Schmidt et al., 1990) and deposited mass along the pleat was measured using electronic microscopy. Results show an influence of the filtration velocity on the deposit.