To ensure a drug product that is safe, reliable and effective, quality assurance and control plays a vital role in pharmaceutical manufacturing and research. Chromatographic techniques have been extensively used as an important analytical tool for the separation, identification and quantification of drugs at various stages of the pharmaceutical process. The main focus of this chapter is on the theory and application of ion-pairing chromatography (IPC) used in the quality control of pharmaceuticals. The theoretical aspect of IPC will describe the currently available theories of this separation. In addition, various types of stationary phases, detectors and mobile phase compositions generally used for analysis of pharmaceuticals utilizing IPC methods will be presented. Furthermore, factors that can affect the retention of analytes by this procedure will be critically evaluated. Application of this technique in the analysis of drugs in biological fluids, raw materials, pharmaceutical formulations and tests designed to assure the stability and performance of the drugs will also be discussed.