Selective synthesis of particles of angstrom to nanometer size consisting of one to many metal atoms is instrumental in various applications, but it has been hampered by the tendency of the metal atom to form large clusters. We found, as studied by the state-of-the-art electron microscopic technique, a strategy to produce metal-containing nanoparticles isolated from each other by depositing metal atoms in a hydrophilic hole on or in the interior of a carbon nanotube as demonstrated by the reaction of Gd(OAc)(3) with oxidized single-wall nanohorns. Besides the potential utilities of the deposited metal clusters, the metal deposition protocol provides a method to control permeation of molecules through such openings.