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Hydrophobic nanostructured silica (SiO2) particles were synthesized from sprayed droplets of a colloid containing SiO2 nanoparticles, a surface modifier and a solvent by aerosol assisted self-assembly. Trimethylchlorosilane (TMCS) and ethyl alcohol were used as a surface treating agent and a solvent, respectively. Morphology, pore size distribution, specific surface area, chemical bonds, and hydrophobicity of the self-assembled particles were analyzed. The self-assembled particles were spherical in shape and composed of micro, meso and macro pores. Average diameter of the product particles was around 2 μm. The pore size distribution of the particles ranged from 1.5 to 200 nm. The degree of methanol wettability representing hydrophobicity of the product particles was directly proportional to TMCS concentration and ranged from 35 to 58%.