This work focuses on the synthesis, functionalization, and application of gold and silver nanoparticles, magnetic nanoparticles Fe3O4, combination of 4-ATP-coated silver nanoparticles and Fe3O4 nanoparticles. The synthesis methods such as chemical reduction, seeding, coprecipitation,and inverse microemulsion will be outlined. Silica- and amino-coated nanoparticles are suitable for several applications in biomedicine and the environment. The applications of the prepared nanoparticles for early detection of breast cancer cells, basal cell carcinoma, antibacterial test, arsenic removal from water, Herpes DNA separation, CD4+ cell separation and isolation of DNA of Hepatitis virus type B (HBV) and Epstein-Barr virus (EBV) are discussed. Finally, some promising perspectives will be pointed out.