Implant surface properties define the interaction of the implant with the surrounding tissue. To obtained advanced biological, mechanical and physical properties, metallic implants are often exposed to different kinds of surface modification. The electrochemical anodization process is an efficient method for nanostructured surface modification, which leads to the formation of nanotubular oxide layers on metallic surfaces. These obtained layers could be applied in biomedicine due to their chemical stability, biocompatibility and non-toxic nature in the human body. As a part of different kinds of medical implants such as dental implants, artificial hip joints, bone plates, screws, spinal fixation devices or stents, an oxide layer significantly increases cells adhesion and plays a significant role in improving the rate of osseointegration. However, an important topic in research of implants with a nanotubular oxide layer is integrity during fixation and exploitation and possible damage initiation and development. This review article aims to present the application of nanotubular oxide layers in biomedicine and to explain their influence on the biocompatibility and osseointegration of medical implants. Influence of the layers properties, such as roughness or contact angle, and the influence of their morphology on biocompatibility and osseointegration, as well as the influence of fixation and exploitation on the damage of the nanotubular oxide layer, are considered.