The conventional methods of downstream purification of a recombinant protein are not only complicated and delicate but time consuming, and need to be improved. Since the intein, the protein splicing element, was discovered, this self-cleaving element has been exploited and applied to the purification of recombinant proteins which could significantly simplify the purification procedure. Intein has the unique property that when it is combined with an affinity tag, it enables a target protein to be purified in a single chromatographic step. This review elucidates the properties of intein (the mechanism that unravels the intein-based protein splicing), the advantages of an intein affinity expression system, the progress of intein-based protein purification procedures, and recent advances in the applications of intein. Further development of the intein-based purification system may lead to the applications of this system to industrial-scale production of recombinant proteins. (C) 2009 Society of Chemical Industry