The use of polyelectrolytes as mobile affinity matrices in electrophoresis has led to the development of a specific separation method for biological molecules, affinophoresis. The conjugate of a polyelectrolyte and an affinity ligand is called an affinophore. Electrophoresis of proteins in the presence of an affinophore results in a change in the mobility of a specific protein by the formation of a specific complex through the affinity of the protein to the ligand. Polylysine is useful as a base polymer of affinophores and has been used successfully as an anionic matrix after succinylation. Affinophoresis of proteases, lectins and antibodies has been carried out in agarose gel and the mobility of the proteins having affinity to each ligand was specifically changed. Two-dimensional affinophoresis, in which an affinophore was included only in the second-dimensional electrophoresis, was effective for the identification of the molecule having affinity to the affinophore in a complex mixture. The use of capillary electrophoresis highlighted the relevance of affinophoresis in quantitative analyses of molecular interactions, allowing the determination of affinity constants with small amount of samples and with high precision.