Thymidine receptor residues were covalently attached to the inner side wall of silica nanotubes (SNTs). The adsorption capacities of the thymidine-functionalized silica nanotubes (T-SNTs) with nucleic acids and oligonucleic acids were evaluated. The T-SNTs exhibited excellent selectivity both in recognition and separation of adenosine and adenosine-based oligonucleotides, because adenosine and oligoadenosine were selectively bound to the inner surface of T-SNTs by formation of complementary intermolecular hydrogen bonds. On the other hand, guanosine, cytosine and oligoguanosine derivatives were not bound to the T-SNTs. The T-SNTs selectively separated 95% of oligoadenosine from a mixture of equal amounts of oligocytosine and oligoguanosine. Our results imply that the T-SNTs can be used as a selective receptor and separator for the extraction and separation of adenosine and oligoadenosine derivatives in aqueous solution.