The best way to preserve the mechanical properties of bone specimens is hydration in NaCl, whereas the reference process in microCT analysis is defatting. However, for finite element modelling (FEM) it is necessary to use the same bone specimens for biomechanical testing and 3D imaging. This study aimed to evaluate the effect of sample conditioning on trabecular bone microarchitectural parameters. Trabecular bones were analysed by microCT under three successive conditions: first, the fatted samples were analysed immersed in NaCl (process N); second, they were hydrated for 24 h then imaged without immersion (process H); third, the samples were defatted before analysis (process D). The microarchitectural parameters bone volume/tissue volume (BV/TV), trabecular spacing (Tb.Sp), number (Tb.N) and thickness (Tb.Th) were calculated. Except for BV/TV, there was no significant difference between the processes N and D. In process H, BV/TV, Tb.Th and Tb.N were higher and BS/BV and Tb.Sp were lower than in process D. Results showed that the process D may be replaced by the process N. The process H induced significant differences in microarchitectural parameters when compared to process D. Nevertheless, this sample conditioning should be used to develop FEM when microCT images are to be acquired during compressive testing.