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α- and γ-cyclodextrin in columnar structures with only water molecules included were successfully obtained by appropriate recrystallization from their aqueous solutions. These crystals were found to adopt a channel-type structure similar to the cyclodextrin inclusion compounds formed with guest polymers. Experimental investigations of their inclusion properties demonstrate that only α-cyclodextrin in the columnar structure (α-CDcs) is able to include both small molecules and polymers. Thermal measurements reveal that columnar structure α-CDcs contains three different types of water molecules. The most strongly held water molecules are located outside of the cyclodextrin cavity, likely hydrogen-bonded between the rims of neighboring cyclodextrins in the columnar α-CD stacks. X-ray analyses confirm that the channel structure is preserved in the dehydrated α-CDcs and its inclusion compounds formed with various guests. In contrast, a completely different behavior was observed for γ-CDcs in the columnar structure. It appears that α-CDcs, at least, can function as a nanoscopic filter for separating both small molecules and polymers on the basis of their abilities to be included, or not, in the narrow (∼0.5 nm) channels of the α-CDcs crystals.