Ion exchange chromatography separates charged molecules from a solution by reversibly exchanging them with mobile, or 'active', ions associated with the oppositely charged stationary phase. This method can be used to separate ions, soften and deionize water, and purify solutions. The polymers comprising the ion-exchange column are high-molecular-weight and chemically stable polymers, crosslinked to be porous and essentially insoluble. They are also functionalized with either acidic or basic groups. When functionalized with acidic groups, the columns or resin are known as cation exchangers and contain negatively charged polymers with positive counter ions. These allow cations to be exchanged from the mobile phase. When functionalized with basic groups, the columns or resin are known as anion exchangers, which contain positively charged polymers with negative counter ions and exchange anions from the solution.

During ion exchange, the counterions associated with the solid-phase polymers enter the solution while ions from the solution interact with the polymer in their place. Note that the ability to exchange ions increases as the extent of cross-linking increases and the number of ion-exchange groups increases in the polymer. This exchange is reversible and continues until equilibrium is established.

Acid cation exchangers can be functionalized with either strong acids, such as sulfonic acid (−SO₃H), seen in polystyrene sulfonic acid, or weak acids, such as carboxylic acid (−COOH), seen in poly(methyl methylacrylic) acid. Similarly, anion exchangers are classified as either strong or weak. Strong anion exchangers often contain quaternary ammonium groups (−CH₂N(CH₃)₃⁺), such as those in polystyrene quaternary ammonium chloride, and weak anion exchangers are often functionalized with substituted amines (−NH₃⁺), such as those in polystyrene tertiary amine hydroxide.