Nanoparticles (NPs) of noble metals such as silver (Ag NPs) or gold (Au NPs) draw the attention of scientists looking for new compounds to use in medical applications. Scientists have used metal NPs because of their easy preparation, biocompatibility, ability to influence the shape and size or modification, and surface functionalization. However, to fully use their capabilities, both the benefits and their potential threats should be considered. One possibility to reduce the potential threat and thus prevent the extinction of their properties resulting from the agglomeration, they are covered with a neutral material, thus obtaining core-shell nanostructures that can be further modified and functionalized depending on the subsequent application. In this review, we focus on discussing the properties and applications of Ag NPs and Au NPs in the medical field such as the treatment of various diseases, drug carriers, diagnostics, and many others. In addition, the following review also discusses the use and potential applications of Ag@SiO2 and Au@SiO2 core-shell nanostructures, which can be used in cancer therapy and diagnosis, treatment of infections, or tissue engineering.