We have carried out co-assembly of N-(11-cis-octadecenoyl)-β-D-glucopyranosylamine 1 with hydrophobic molecules, 8-anilinonaphthalene-1-sulfonate (1,8-ANS) 2 or Zn-phthalocyanine 3 in a mixed solvent of organic solvents and water to form nanotubes embedding the hydrophobic molecules. Transmission electron microscopic (TEM), fluorescence microscopic observations, and X-ray diffraction (XRD) analysis revealed the formation of nanotubes where the interdigitated bilayer membranes of 1 function as an embedded matrix for the hydrophobic molecules. We have compared the release behavior of 2 embedded in the bilayer membranes with that of 2 encapsulated inside the nanotube hollow cylinder of 60-nm inner diameter. Although the encapsulated molecules 2 proved to be slowly released from both open ends of the hollow cylinder at room temperature, the embedded ones kept staying in the bilayer membranes. Similarly, the embedded molecules 3 kept staying in the interdigitated bilayer membranes at temperatures below a thermal phase transition temperature (T_g-l = 59 °C) of the nanotubes. However, when the solid-state bilayer membranes of the nanotubes converted into a fluid bilayer membrane at temperatures above the T_g-l, the molecules 3 was instantly released. Such self-assembled nanotubes embedding hydrophobic molecules are applicable to medical diagnosis systems containing deliveries of drugs, photosensitizers, fluorescence- and spin-probes.