Since few years, several quantum transport experiments employing unimolecular systems have been proven. Some of related emerging phenomena, however, are still missing sound theoretical explanations. One principal limitation is the `static' description of molecular bridges typically assumed for transport processes. Molecules, indeed, are flexible objects and their nuclear `dynamics' plays in general a fundamental role in charge transfer as well as transport mechanisms. In this talk, I will give an overview on the role of vibrations and inelastic transport in molecular systems, and show how such phenomena do dramatically affect the overall conduction properties of molecular junctions.