Chromatography is commonly used to separate mixtures into their individual components. Most commonly, this involves separating a mixture dissolved in a liquid solvent, by passing the solution over a solid surface, with the components moving at different rates depending on their affinity for the surface. In ion chromatography, ions and polar molecules are separated based on charge relative to an ion exchanger. It is often used to separate proteins, nucleotides and amino acids, for water analysis, and for detecting anions in blood samples. The solution of the mixture in the solvent is known as the mobile phase and the solid surface is known as the solid phase.

Ions are electrically charged atoms or molecules. They are charged because they have either gained electrons (negatively charged) or lost electrons (positively charged). Anions are negatively charged ions, which have gained electrons. Cations are positively charged ions, which have lost electrons. Ion chromatography can be either anion-exchange or cation-exchange. In cation-exchange chromatography, the stationary phase is negatively charged in order to attract the positively charged ions. Conversely, anion- exchange chromatography uses a positively changed stationary phase to attract the negatively changed ions.

When ion chromatography is used for water analysis, it can detect the presence of substances in the parts-per-billion range. Major anions include fluoride, chloride, nitrate, nitrite, and sulfate, while major cations include lithium, sodium, ammonium, potassium, calcium, and magnesium. This can be useful for analyzing drinking water for pollution, understanding water chemistry in ecosystems, and determining the nutrients in food. Heavy metals and transition metals such as lead, copper and cadmium may also be detected in drinking water using this technique.

A common clinical use of ion chromatography is to monitor blood sulfate levels. Other important anions which may be detected in blood include chloride and phosphate.

Before carrying out ion chromatography, samples are filtered to remove particulates such as sediment, as well as micro organisms. Typically a digital device known as an ion chromatograph is used, this consists of modules to control flow rate, pumps, the analytical column, and the detector module. It is typically interfaced through its own software running on a standard PC. The instrument will typically detect the level of ions at different stages in the analytical column using conductivity detectors.