The aim of the study was to investigate whether a fatigue induced weakening of cortical bone was revealed in microstructure and mechanical competence of demineralized bone matrix. Two types of cortical bone samples (plexiform and Haversian) were use. Bone slabs from the midshaft of bovine femora were subjected to cyclical bending. Fatigued and adjacent control samples were cut into cubes and demineralized in ethylenediaminetetraacetic acid. Demineralized samples were either subjected to microscopic quantitative image analysis, or compressed to failure (in longitudinal or transverse direction) with a simultaneous analysis of acoustic emission (AE). In fatigued samples porosity of organic matrix and average area of pores have risen, along with a change in the pores shape. The effect of fatigue depended on the type of the bone, being more pronounced in the plexiform than in Haversian tissue. Demineralized bone matrix was anisotropic under compressive loads in both types of cortical structure. The main result of fatigue pretreatment on mechanical parameters was a significant decrease of ultimate strain in the transverse direction in plexiform samples. The decrease of strain in this group was accompanied by a considerable increase of the fraction of large pores and a significant change in AE energy.