Nanoparticles, the building blocks of nanotechnology, have been widely utilized in various biomedical applications, such as detection, diagnosis, imaging, and therapy. However, another emerging, albeit under-represented, area is the employment of nanoparticles as tools to understand cellular processes (e.g., oxidative stress-induced signaling cascades). Such investigations have enormous potential to characterize a disease from a different perspective and unravel some new features that otherwise would have remained a mystery. In this review, we summarize the intrinsic biological properties of unmodified as well surface modified nanoparticles and discuss how such properties could be utilized to interrogate biological processes and provide a perspective for future evolution of this field.