Affinity chromatography has the reputation of a more expensive and less robust than other types of liquid chromatography. Furthermore, the technique is considered to stand a modest chance of large-scale purification of proteinaceous pharmaceuticals. This perception is changing because of the pressure for quality protein therapeutics, and the realization that higher returns can be expected when ensuring fewer purification steps and increased product recovery. These developments necessitated a rethinking of the protein purification processes and restored the interest for affinity chromatography. This liquid chromatography technique is designed to offer high specificity, being able to safely guide protein manufactures to successfully cope with the aforementioned challenges. Affinity ligands are distinguished into synthetic and biological. These can be generated by rational design or selected from ligand libraries. Synthetic ligands are generated by three methods. The rational method features the functional approach and the structural template approach. The combinatorial method relies on the selection of ligands from a library of synthetic ligands synthesized randomly. The combined method employs both methods, that is, the ligand is selected from an intentionally biased library based on a rationally designed ligand. Biological ligands are selected by employing high-throuphput biological techniques, e.g. phage- and ribosome-display for peptide and microprotein ligands, in addition to SELEX for oligonucleotide ligands. Synthetic mimodyes and chimaeric dye-ligands are usually designed by rational approaches and comprise a chloro-triazinlyl scaffold. The latter substituted with various amino acids, carbocyclic, and heterocyclic groups, generates libraries from which synthetic ligands can be selected. A ‘lead’ compound may help to generating a ‘focused’ or ‘biased’ library. This can be designed by various approaches, e.g.: (i) using a natural ligand-protein complex as a template; (ii) applying the principle of complementarity to exposed residues of the protein structure; and (iii) mimicking directly a natural biological recognition interaction. Affinity ligands, based on the peptide structure, can be peptides, peptide-mimetic derivatives (<30 monomers) and microproteins (e.g. 25–200 monomers). Microprotein ligands are selected from biological libraries constructed of variegated protein domains, e.g. minibody, Kunitz, tendamist, cellulose-binding domain, scFv, Cytb₅₆₂, zinc-finger, SpA-analogue (Z-domain).