Nanotechnology has been considered as a promising strategy for diagnosis and treatment of various diseases. However, the stability and circulation times of the conventional nano-carriers, such as liposomes and micelles, are still unsatisfied. Perfluorocarbons (PFCs) are biologic inert synthetic materials, which are highly hydrophobic and have a tendency to self-aggregation. Additionally, PFCs themselves can act as 19F magnetic resonance imaging agents and oxygen carriers. Thus, the construction of the fluorinated carriers will not only improve the stability of the carriers, but also endow them with additional functions. Here we review the recent advances of PFC-based nanosystems for diagnosis and treatment of diseases.