A novel technique, frontal analysis continuous capillary electrophoresis (FACCE), has been described as an effective way to study protein-polyelectrolyte binding. FACCE involves continuous sampling, integrating sample injection and separation into one process that provides advantages over conventional frontal chromatography. The method provides rapid and precise determination of binding isotherms, and allows for quantitative binding analysis in terms of binding constant and the binding-site size by considering the protein as the ligand and allowing the polyelectrolyte to bind to a number of proteins with variable levels of cooperativity. FACCE is particularly suitable for binding systems involving rapid binding kinetics because it allows for the determination of the concentrations of free or bound ligands under conditions that avoid perturbation of the binding equilibrium. This chapter focuses on studies of the binding of bovine serum albumin (BSA) to heparin using FACCE. These investigations are demonstrated within the context of this chapter as representative of a model protein-polyelectrolyte system from which extensions to other systems can be made.