Abstract: Molecular electronics is the study of charge transport through single molecules or molecular ensembles. Molecular electronic junctions consist of single molecules or an ensemble of molecules positioned between two conducing contacts. To fabricate and measure the electronic properties of molecular junctions, several techniques have been employed such as scanning tunneling microscopy, conducting probe atomic force microscopy, and vapor deposition of top contacts. Charge transport observed through molecular junctions has been shown to exhibit technologically important phenomena such as rectification, conductance switching, and orbital gating. The primary focus of the field of molecular electronics is to understand the effect of molecular properties, such as structure and molecular orbitals, on charge transport mechanisms through molecular junctions. In this dissertation, the various techniques to fabricate and characterize molecular junctions are discussed, along with an introduction to charge transport mechanisms expected to control transport through molecular junctions. More specifically, this dissertation is primary focused on the fabrication and characterization of molecular junctions fabricated through the formation of an electronic contact on a molecular layer through physical vapor deposition. A common problem with this technique is structural damage to the molecular layer or metal penetration through the molecular layer during the contact formation. To overcome these limitations, a novel fabrication technique was developed and employed to fabricate reproducible molecular junctions through a physical vapor deposition technique without molecular damage or metal penetration. Termed surface diffusion mediated deposition (SDMD), the technique remotely deposits a metallic contact adjacent to and about 10 - 100 nm away from the molecular layer. Surface diffusion causes the metallic contact to migrate towards and onto the molecular layer to form an electronic contact. With SDMD, single molecule and many-molecule junctions are fabricated and electronically characterized. To probe electronic states and molecular structure in molecule/oxide junctions, an in-situ optical absorbance spectroscopy technique was developed and employed to monitor bias induced molecular redox events in solid-state molecular junctions. Correlation of the observed spectral changes with molecular redox events allows characterization of the electronic properties of molecules which are critical in understanding charge transport through molecules. In a related application, the developed in-situ optical absorbance spectroscopy technique was used to probe doping events in polypyrrole/oxide junctions. Doping reactions in polypyrrole are shown to strongly depend on the surrounding environment. For application to both molecular and conjugated polymer junctions, in-situ absorbance spectroscopy is shown to be a useful analytical tool to determine charge transport mechanisms. Finally, a thermal oxidation technique is introduced to increase the resolution of nanoimprint lithography to fabricate nanogap electrodes for molecular junctions. The advantage of this technique is the ability to use a simple, fast, and reliable oxidation process to increase the resolution of standard nanofabrication techniques.