Two fabrication methods have been investigated to synthesize silicon oxide nanowires. One was catalytic thermal evaporation method in which silicon monoxide was used as the precursor and Au particles served as the catalysts. Using nanosphere lithography, patterned nanowires were obtained and their growth positions were controlled by the locations of Au catalysts. For the second method, without silicon monoxide as the precursor and without the aid of Au catalyst, silicon oxide nanowires directly formed along the <110> direction of the silicon substrate only with the introduction of hydrogen gas. A series of experiments were carried out to study effects of reaction time, temperature, and hydrogen on the growth of the nanowires. Also, various electron microscopy techniques were utilized to characterize their morphologies and internal structures and to analyze their compositional distributions. In this paper, the characterization of different silicon oxide nanowires and their formation mechanisms in relation to both preparation methods are discussed.