The development of analytical methodologies to elucidate mechanisms of peptide transport and metabolism is important for the understanding of disease states and the design of effective drug therapies. Interest in the use of microchip capillary electrophoresis (CE) devices for peptide analysis stems from the ability to perform fast, highly efficient separations combined with small sample volume requirements. Many of the separation modes developed on conventional systems, including electrochromatography, isoelectric focusing, and electrophoretic bioaffinity assays, have been demonstrated on microchip devices. Steps that include sample preparation and labeling can also be integrated onto the microchip platform. This chapter will discuss considerations for peptide analysis using microchip CE and will focus on different approaches to sample preparation, separation, and detection.