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Abstract: Molecularly imprinted cyclodextrins were applied to HPLC stationary phases for efficient recognition of nano-scaled guests in water. When cholesterol was used as a template molecule, the imprinted polymer selectively retained this guest more strongly and selectively than did non-imprinted polymer. The imprinting effect in the retention behavior was consistent with previously reported physicochemical analyses. Immobilization of the imprinted cyclodextrin polymer on the surface of silica gel in water was also successful. The polymer-silica gel composites obtained had sufficient physical strength, and were useful for HPLC stationary phases. These molecularly imprinted polymers could recognize steroids, amino acid derivatives, dipeptides, and antibiotics. Moreover, we found that the enantio-selectivity toward the template molecules was significantly promoted. This methodology has great potential for the recognition of large guest molecules in water, and can be an alternative to affinity chromatography for the separation of bio-molecules