Separation of amino acids, peptides, and proteins (bioanalytes) via ion exchange (IE) has widespread usage because it is usually very simple to design and it has high capacity and easily achievable control of the separation process. Amino acids, as principal constituents of proteins and having a plethora of biological functions of their own, are always in focus when developing novel methods. Separation and quanti fi cation of amino acids is essential in food science, medicine, agricultural science, etc. Peptides exist in nature and have diverse functions. Digestion of proteins by enzymes also gives complex mixtures of peptides and IE fi nds its application in peptide separation. There are lots of reasons for the popularity of IE in protein isolation and puri fi cation. It is used in research, analysis, and large-scale puri fi cation of proteins. Ion exchange is ideal for the initial capture of proteins because of its high capacity, relatively low cost, and its ability to survive rigorous cleaning regimes. This chapter covers basic principles and modern applications of IE in separation of amino acids, peptides, and proteins.