Recognition at the molecular level is a fundamental characteristic of biochemical systems. Recent models developed in bioorganic chemistry have revealed the importance of complementarity in size, shape, and functional groups in molecular recognition. Structures that feature a cleft are particularly effective in regard to complementarity since functional groups attached to the interior of the cleft converge on substrates held inside. The molecular clefts offer the advantage of efficient construction; their surfaces can be tailored for specific applications. This article describes their use for recognition of acids, bases, amino acids, metal ions, and neutral substrates. Their ability to provide microenvironments complementary to asymmetric molecules and their future promise are discussed.