Abstract Surface nanostructures like titanium oxide nanotubes and nanopores have revealed excellent functionalization performance and good corrosion resistance. In certain cases, biodegradability is, however, an advantageous feature for implant materials. Recently iron-based materials have been studied as promising degradable biomaterials. In order to functionalize biodegradable iron-based materials, oxide nanostructured arrays have been used as a surface functionalization approach. In this study, two different iron oxide nanostructures, nanopores and nanotube arrays with different thicknesses, were fabricated on pure iron by an anodization method. The influence of anodization conditions on the morphology of the novel nanostructures was investigated. The degradation behavior is essential to the biomedical application of iron oxide nanostructured arrays. Hence electrochemical and immersion tests in simulated body fluid (SBF) solution were conducted to reveal details and the mechanism of the degradation process. Surface composition and morphology of immersed iron oxide nanostructures were investigated. Furthermore, indirect contact cell experiments were carried out by employing extracts from immersion solution of iron oxide nanostructures on human osteoblast-like MG-63 cells. Results of the in vitro tests indicated no cytotoxicity caused by the extracts of the nanoarrays on pure iron. The current understanding of the degradation process and cytocompatibility of iron oxide nanostructures gained from this work is essential for their further study and for considering biomedical application of such nanostructures.