Molecular recognition-based separation and sensing systems have received much attention in various fields because of their high selectivity for target molecules. Molecular imprinting has been recognized as a promising technique for the development of such systems, where the molecule to be recognized is added to a reaction mixture of a cross-linker(s), a solvent(s), and a functional monomer(s) that possesses a functional groups(s) capable of interacting with the target molecule. Binding sites in the resultant polymers involve functional groups originating from the added functional monomer(s), which can be constructed according to the shape and chemical properties of the target molecules. After removal of the target molecules, these molecularly imprinted complementary binding sites exhibit high selectivity and affinity for the template molecule. In this article, recent developments in molecularly imprinted polymers are described with their applications as separation media in liquid chromatography, capillary electrophoresis, solid-phase extraction, and membranes. Examples of binding assays and sensing systems using molecularly imprinted polymers are also presented.