Nanocontainers such as mesoporous silica particles and polymersomes are versatile structures containing holes or pores which are used for the entrapment of small molecules and the introduction of specific functionalities. They are widely applied in drug delivery, biomedicine, bioreactors, and analytical applications. In the last case, nanocontainers usually serve as amplification systems. They are hence synthesized to entrap signaling molecules and to bear functional moieties at the outer surface, which in turn enable specific analyte recognition and control of the nanocontainer pore permeability. This Review outlines the most important nanocontainer materials and discusses their synthesis, surface chemistry modifications, and strategies for molecule entrapment. Their advantages, challenges, and limitations are critically discussed in view of other common signal amplification strategies for different assay formats and various detection methods.