Polymers that respond to small changes in environmental stimuli with large, sometimes discontinuous changes in their physical state or properties, are often called “smart” polymers. Poly(N-isopropylacrylamide), PNIPAAm, is one of the most representative smart polymer that exhibits a thermally reversible soluble-insoluble change in the vicinity of its lower critical solution temperature (LCST) at 32°C in aqueous solution. Temperature-responsive chromatography for the separation of biomolecules utilizing the poly(N-isopropylacrylamide) (PNIPAAm)-modified stationary phase is performed with an aqueous mobile phase without using an organic solvent. The surface properties and function of the stationary phase are controlled by external temperature changes without changing the mobile-phase composition. The separation of the biomolecules, such as nucleotides, was achieved by a dual temperature- and pH-responsive chromatography system. The electrostatic and hydrophobic interactions could be modulated simultaneously with the temperature in an aqueous mobile phase. Additionally, we also prepared functional copolymers composed of N-isopropylacrylamide (NIPAAm) and amino acid derivative or naphthyl alanine derivative, which have temperature-responsiveness and molecular recognition. These separation systems would have potential applications in the separation of biomolecules.