Molecular transport junctions, in which electrons transit molecules under the application of an external voltage bias, are a subject of intense current interest for both practical applications and the fundamental understanding of electronic transport at the nanoscale, since they can show striking nonlinear effects, such as negative differential resistance, and switching accompanied by hysteresis. A full understanding of these phenomena requires detailed microscopic characterization of the active region of the junction, which has to date been lacking. However, the last few years have seen the resurgence of tunneling spectroscopy as a premiere analytical tool for investigating nanoscale and molecular junctions. Inelastic Electron Tunneling Spectroscopy (IETS) due to localized molecular vibrational modes was discovered in 1966 by Jaklevic and Lambewhen they studied the tunneling effect of metal–oxide–metal junctions. Instead of finding band structure effects due to metal electrodes as they initially hoped, they observed patterns in the characteristics which were related to vibrational excitations of molecular impurities contained in the insulator, IETS has since been developed into a powerful tool for various applications such as chemical identification, bonding investigation, trace substance detection, etc