This study aims to provide an initial database to gain more detailed knowledge of the trabecular and cortical bone structure of pelvic and femur bones in cats and smaller dogs. Additionally, the bony microarchitecture between cats and smaller dogs was compared to identify possible differences between those species. These findings could potentially improve the development of non-cemented total hip replacement (THR). To determine the bony microarchitecture, a total of 48 pelvises and thus 96 acetabuli and femora of smaller dogs (n = 21) and cats (n = 27) were analysed using microcomputed tomography. The parameters bone volume (BV/TV), bone surface (BS/BV), trabecular thickness (Tb.Th), number of trabeculae (Tb.N), trabecular spacing (Tb.Sp), degree of anisotropy (DA), connectivity density (Conn. D) and mean bone density were measured and compared between the species. In addition, the femoral angle of antetorsion was determined on both sides of the body. Overall, cats had fewer but thicker trabeculae than the small dogs in the analysed areas of the pelvis and femur. This resulted in a greater trabecular distance in cats than in small dogs. Together with a higher cortical bone density at the femoral shaft in cats, it could be determined that cats have a more stable bone architecture in the measured areas than smaller dogs. The angle of antetorsion did not differ significantly between the cats and the dogs examined.