Stainless steel membranes have been coated by using the ion beam assisted deposition technique with BN thin films : some deposited films exhibit the cubic microcrystalline structure (c-BN) while others exhibit the hexagonal one (h-BN). The samples have been submitted to deuterium permeation tests and in a second step they have been analysed by elastic recoil detection (ERD). It was observed that the permeation flux transient is sensible to the structure of the deposited layers as suggested by the different shape of the permeation curves pertinent to the h-BN or to the c-BN coated samples. These different shapes have been attributed to deuterium trapping processes in the BN layers with the hexagonal structure : the higher deuterium content in the h-BN than in the c-BN, after permeation, as revealed by ERD analysis, is consistent with the previous observation.