The extreme miniaturization trend of electronic devices is following a pace that, if maintained, would imply that in twenty years transistors would reach the size of small organic molecules. As far as fundamental science is concerned this limit has been already reached: Rectifying properties of single molecular devices have been already experimentally proved. Quantum transport at the molecular scale, however, still lacks a satisfactory theoretical description of the relevant molecular conduction mechanisms. One reason is that vibrational effects are typically neglected: ``static'' descriptions of transport processes are typically considered. 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 of our recent research in Regensburg in the Molecular Computing Group 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.