Reversed phase high performance liquid chromatography (RP-HPLC) now plays a critical role in the analysis and purification of peptides and proteins from natural and synthetic sources. The extraordinary popularity of RP-HPLC for polypeptide analysis can be attributed to a number of factors hi9ghlighted in this chapter. Some of the potential of RP-HPLC in the purification of polypeptides and proteins is demonstrated by the selected samples. Despite the current wide usage of RP-HPLC techniques in protein sequencing studies and many other purification areas involving high resolution polypeptide separations, the selection of a particular chemically-bonded stationary phase and mobile phase composition has frequently been based on empirical criteria. Not uncommonly, such arbitrary selections may not adequately address the issues of optimal chromatographic resolution, band shape or solute recovery. This chapter documents recent theoretical developments which characterize the RP-HPLC of polypeptides and proteins, and describes recent advances in the evolution of fully mechanistic models which describe in physicochemical terms the nature of the interaction between biological macromolecules and biological and synthetic surfaces.