Nanomaterials can display distinct biological effects compared with bulk materials of the same chemical composition. The physico-chemical characterization of nanomaterials and their interaction with biological media are essential for reliable studies and are reviewed here with a focus on widely used metal oxide and carbon nanomaterials. Available rat inhalation and cell culture studies compared to original results suggest that hazard potential is not determined by a single physico-chemical property but instead depends on a combination of material properties. Reactive oxygen species generation, fiber shape, size, solubility and crystalline phase are known indicators of nanomaterials biological impact. According to these properties the summarized hazard potential decreases in the order multi-walled carbon nanotubes >> CeO2, ZnO > TiO2 > functionalized SiO2 > SiO2, ZrO2, carbon black. Enhanced understanding of biophysical properties and cellular effects results in improved testing strategies and enables the selection and production of safe materials.