Determination of the pharmacokinetics and metabolite identification have been an integral part of drug discovery and development to ensure that drugs have appropriate absorption, distribution, metabolism and excretion properties. Liquid chromatography interfaced with a mass spectrometer has greatly facilitated these studies. Nano-electrospray has distinct sensitivity advantages and the increased amount of time available to perform mass spectrometric experiments facilitates structural characterization of metabolites. The recently developed silicon chip-based nano-electrospray devices are more practical than pulled capillaries. The use of these devices for the determination of pharmacokinetics and metabolite identification will be described and particular attention will be paid to the distinct advantages and disadvantages these devices offer.