This review article is aimed at assessing the recent progress made in affinity nano-LC and affinity CEC performed in capillaries and microchips. A variety of biospecific interactions is covered including lectin affinity, immunoaffinity, immobilized metal affinity, sugar-based affinity, protein A affinity, protein G affinity, aptamer affinity, enzyme affinity, and other miscellanea. ACE involving affinity interaction in free solution is not covered in this review article. Also, affinity-based separations involving chiral recognition are not the subject of this review article because they are the topic of a more specialized review article on chiral separations in this special issue. A total of 31 papers published in the period 1998-2006 have been discussed in this review article.