With the growing interest in the applications of gold nanoparticles in biotechnology and their physiological effects, possible toxicity of gold nanoparticles is becoming an increasingly important issue. A large number of studies carried out over the past few years under a variety of experimental conditions and following different protocols have produced conflicting results, leading to divergent views about the actual safety of gold nanoparticles in human applications.This work is intended to provide an overview of the most recent experimental results and thereby summarize current state-of-the-art. Rather than presenting a comprehensive review of the available literature in this field, which would be impractically broad, we have selected representative examples of both in vivo and in vitro studies, which clearly demonstrate the need for urgent and rigorous standardization of experimental protocols. Despite their significant potential, the safety of gold nanoparticles is highly controversial at this time, and important concerns have been raised that need to be properly addressed. Factors such as shape, size, surface charge, coating, and surface functionalization are expected to influence the interactions of particles with biological systems to a different extent, resulting in different outcomes and influencing the potential of gold nanoparticles for biomedical applications.Moreover, despite continuous attempts to establish a correlation between structure of the particles and their interactions with biological systems, we are still far from elucidating the toxicological profile of gold nanoparticles in an indisputable manner. This review is intended to contribute towards this goal, offering a number of suggestions on how to achieve the systematization of data on the most relevant physico-chemical parameters, which govern and control the toxicity of gold nanoparticles at cellular and whole-organism levels.