Modern molecular targeting provides new opportunities for imaging, diagnosis and treatment of diseases. Small molecular weight peptides have the potential for enhancing targeting of compounds, and they may also have therapeutic effects by themselves. The limiting step for successful molecular targeting is the development of efficient peptide delivery systems. This review will focus on peptides developed by phage display and combinatorial chemistry for the delivery of pharmaceuticals, radioactive compounds and gene expression vectors. Target cell-specific delivery can be improved by peptides that penetrate the cell membrane or alternatively induce receptor-mediated endocytosis. In addition, peptides that contain endosomal escape signals or nuclear localization motifs may help trafficking of therapeutics to appropriate locations inside the cell. Small molecule radiolabelled peptides are the preferred agents for targeting and for diagnostic imaging of various organs as they are easily synthesized, effectively penetrate tissues, and are rapidly cleared from the circulation. Such peptides have been tested in animals and humans in the fields of cancer, cardiology, neurology, inflammation / infection, atherosclerosis and thrombosis.