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This paper describes three-dimensional micro-self-assembly using hydrophobic interaction. The interaction between microparticles was controlled using self-assembled monolayers formed on the particles. The particles were stirred in a dispersion liquid to create a binding for connecting their surfaces directly. The interaction between the particles was described by the thermodynamic free energy of adhesion, which was calculated using the surface free energies of the solids and the liquid. The calculated free energy was then used to predict the bindings between particles. The binding probability was estimated by counting the number of microparticles that became bound to hydrophobic and to hydrophilic areas patterned on a substrate. The ratio of the bound particles was correlated to the difference between the free energies of the two areas, as predicted using the free energy calculation. This means that microparticle binding is controlled by the surface properties. Structures composed of several microparticles were successfully self-assembled using this principle. Hydrophobic interaction can thus be applied to micro-scale self-assembly.