 In the past decades, much attention has been paid to toxicity assessment of nanoparticles prior to clinical and biological applications. While in vitro studies have been increasing constantly, in vivo studies of nanoparticles have not established a unified system until now. Predictive models and validated standard methods are imperative. This review summarizes the current progress in approaches assessing nanotoxicity in main systems, including the hepatic and renal, gastrointestinal, pulmonary, cardiovascular, nervous, and immune systems. Histopathological studies and specific functional examinations in each system are elucidated. Related injury mechanisms are also discussed.