The caged cell-penetrating peptide (cCPP) conjugates of this invention are ideal for intracellular delivery of a broad variety of cargoes including various nanoparticulate pharmaceutical carriers (liposomes, micelles, microparticles, nanoparticles, polymer-conjugates). The conjugates comprise a detectable agent or a therapeutic agent, and the conjugates provide a novel strategy for site-specific delivery of the same to appropriate tissues in the subject. Versatile application of the conjugates in diagnostics and imaging is described.