Intracellular compartments, in particular the cytoplasm or nucleus, have generally been poorly accessible or inaccessible to radiolabeled biomolecules (e.g., monoclonal antibodies [mAbs], peptides, or oligonucleotides [ODNs]). However, recently cell-penetrating peptides (CPPs) and nuclear localizing peptide sequences (NLSs) have been shown to have the capability of inserting biomolecules into cells and transporting them to the cell nucleus. This discovery now presents intriguing new opportunities to design radiopharmaceuticals that could potentially probe, through imaging, the expression of key intracellular or intranuclear regulatory proteins that define the tumor phenotype, predict outcome, or act as sensitive reporters of response or resistance to treatment. CPPs could also more efficiently internalize radiolabeled antisense ODNs or peptide nucleic acids (PNAs) into tumor cells to enhance the sensitivity of imaging gene expression at the mRNA level. Perhaps one of the most exciting new developments to emerge is the use of NLS to route mAbs and peptides conjugated to nanometer-micrometer range Auger-electron-emitting radionuclides (e.g., (111)In) to the nucleus of cancer cells following their receptor-mediated internalization. In the nucleus, these electrons are highly potent in causing lethal DNA strand breaks. In some cases, NLSs are present naturally in peptide growth factors or their receptors, where they function to deliver internalized ligands to the nucleus, or alternatively, they can be introduced synthetically. This update reviews the properties of CPPs and NLS and focuses on their use for inserting radiolabeled biomolecules into cancer cells for imaging or targeted Auger electron radiotherapy of malignancies.