Among various types of fuel cells, direct methanol fuel cell (DMFC), has been widely investigated in recent years [1]. One of the most important problems associated with DMFC is slow kinetic for oxidation of methanol. At present Pt or Ru or their alloy are the state of the art catalysts for methanol oxidation in DMFC [2]. Pt and PtRu catalysts were synthesized by polyol method in a microwave oven. The synthesis processes of the catalysts and particle size were followed by means of UV/Vis and XRD techniques. The catalysts were prepared by simultaneous or successive reduction of the precursors and the resulting catalysts were treated under different atmospheres and at different temperatures. The electrochemical behavior of the catalysts was investigated by coating them on glassy carbon and carbon paper electrodes. Various electrochemical methods such as cyclic voltammetry, chronoamperometry and linear sweep voltammetry were used for investigation of the effective parameters on the electrocatalytic behavior of the catalysts towards oxidation of methanol, including synthesis parameters such as starting pH, and measuring parameters such as methanol concentration and temperature. The catalysts synthesized at neutral pH, showed better electrocatalytic activity towards methanol oxidation with respect to the other catalysts prepared in acidic and basic pHs. Although XRD spectrum of the PtRu catalyst, which was heat treated under hydrogen atmosphere, showed better alloying of the metals and larger particle size. Electrochemical data suggested better resistance of this catalyst against toxicity aroused from methanol oxidation intermediates. RuPt catalyst, in which, Ru and then Pt have been reduced successively, showed faster kinetics relative to the other catalysts. The resistance of this catalyst toward toxic intermediates was similar to the heat-treated PtRu catalyst which was prepared by simultaneous reduction of both metal ions.