Probing the structure of molecules in a metal-molecule-metal junction under an applied voltage is critical for understanding molecular electron transport properties. We present an approach that allows recording surface-enhanced Raman spectra simultaneously with electrical measurements of a monolayer of molecules in molecular electronic junctions. 1,4-Phenylene diisocyanide in two different types of junctions was used to illustrate the approach. The results show that the molecular integrity was intact in the molecular junctions and under the applied bias. The monolayer sensitivity of the approach provides a new powerful tool for characterizing molecular structure in a molecular electronic junction.