Affinity chromatography relies on the specific and reversible binding of a protein to a ligand bound to the matrix, which is then referred to as an affinity resin. The ligand can either bind directly to the protein of interest or to a tag that is covalently attached to the protein (Histidine, GST ...). Affinity chromatography is often the most robust purification procedure and is generally used in the early stages of the purification process. Depending on the downstream application, affinity purification may be the only chromatographic step necessary to achieve adequate purity.

The proteins can be purified by affinity chromatography in a selective or non-selective manner. In selective affinity chromatography, a ligand specific for a covalently linked protein or tag is used. In non-selective affinity chromatography such as Protein A, G, L for immunoglobulins, or heparin for DNA binding proteins, or lectin for glycoproteins, the ligand binds to a group of proteins with Similar bonding capabilities.