The analytical techniques used for the physical characterization of organic molecular electronic-based devices are surveyed and discussed. These protocols include methods that are used to probe molecular assemblies such as single wavelength ellipsometry, water contact angle goniometry, cyclic voltammetry, infrared spectroscopy, and X-ray photoelectron spectroscopy, and methods used to measure charge transport properties of devices such as scanning tunneling microscopy, and inelastic electron tunneling spectroscopy. Examples from our laboratory and the literature are given for each of these analytical techniques.