Biological monitoring (BM) of engineered nanomaterials (ENM) requires the development of appropriate biomarkers of exposure and early biological effect considering the unusual properties of ENM, such as the ability to translocate from the route of entry, to release ions due to their dissolution (for metal species), and to change their chemical identity upon interaction with biomolecules. Although inflammation and oxidative stress represent the main mechanism of injury for several nanoparticles, specific physico-chemical properties can trigger more complex pathophysiological events. Research on biomarkers of particles and fibers of concern has already generated a large amount of data supporting the validity of intermediate end-points to assess changes before clinically apparent disease occurs. The challenge that remains for the development of biomarkers of exposure for ENM is the lack of specificity of all the biomarkers developed so far. However, advances in the system biology and “-omic” techniques applied to nanotoxicology allow assessment as to whether specific biological pathways are activated/perturbed by specific ENM, thus identifying fingerprints and nano-specific endpoints. While future studies should address the specificity of biomarkers, the priority is to evaluate whether quantitative changes in a battery of sensitive biomarkers can occur in groups of exposed workers.