With the rapid developing of nanotechnology, the use of nanomaterials in medical imaging, disease diagnoses, drug delivery, cancer treatment, gene therapy, and basic research have also progressed quickly. The beneficial uses of nanomaterials may cause human exposure through inhalation, ingestion, skin uptake, and intravenous injection. When nanomaterials interact with biological systems, they may generate adverse biological effects. The possible toxic effects of these nanomaterials are unknown until now. The positive applications in biomedicine as well as the negative biological effects of nanomaterials on cardiovascular, respiratory and other systems are highlighted, the possible mechanisms by which nanoparticles result in cardiovascular and pulmonary morbidity are also discussed, and the possible interaction routes and sequences is farther reviewed. Finally, the perspective of risk assessment of nanomaterials in the future is summarized.