Development of multifunctional nanostructures that can be tuned to codeliver multiple drugs and diagnostic agents to diseased tissues is of great importance. Hierarchically assembled theranostic (HAT) nanostructures based on anionic cylindrical shell cross-linked nanoparticles and cationic shell cross-linked knedel-like nanoparticles (cSCKs) have recently been developed by our group to deliver siRNA intracellularly and to undergo radiolabeling. In the current study, paclitaxel, a hydrophobic anticancer drug, and siRNA have been successfully loaded into the cylindrical and spherical components of the hierarchical assemblies, respectively. Cytotoxicity, immunotoxicity, and intracellular delivery mechanism of the HAT nanostructures and their individual components have been investigated. Decoration of nanoparticles with F3-tumor homing peptide was shown to enhance the selective cellular uptake of the spherical particles, whereas the HAT nanoassemblies underwent an interesting disassembly process in contact with either OVCAR-3 or RAW 264.7 cell lines. The HAT nanostructures were found to "stick" to the cell membrane and "trigger" the release of spherical cSCKs templated onto their surfaces intracellularly, while retaining the cylindrical part on the cell surface. Combination of paclitaxel and cell-death siRNA (siRNA that induces cell death) into the HAT nanostructures resulted in greater reduction in cell viability than siRNA complexed with Lipofectamine and the assemblies loaded with the individual drugs. In addition, a shape-dependent immunotoxicity was observed for both spherical and cylindrical nanoparticles with the latter being highly immunotoxic. Supramolecular assembly of the two nanoparticles into the HAT nanostructures significantly reduced the immunotoxicity of both cSCKs and cylinders. HAT nanostructures decorated with targeting moieties, loaded with nucleic acids, hydrophobic drugs, radiolabels, and fluorophores, with control over their toxicity, immunotoxicity, and intracellular delivery might have great potential for biomedical delivery applications.