The cathode catalysts in low temperature fuel cells are associated with major cell efficiency losses, because of kinetic limitations of the oxygen reduction reaction. Additionally, methanol oxidation at the cathode leads to significant lowering of the efficiency in direct methanol fuel cells, which can be alleviated by use of methanol-tolerant catalysts. In this work, alternative carbon-supported platinum-alloy catalysts were investigated by physical methods. Second, methanol-tolerant ruthenium-selenide catalysts were characterized by physical and electrochemical methods. Besides V-i characteristics and electrochemical impedance spectroscopy as electrochemical methods, physical methods such as X-ray photoelectron spectroscopy, nitrogen adsorption, porosimetry by mercury intrusion and temperature programmed reduction are used to characterize the catalysts. The electrochemical characterization yields information about properties and behavior of the catalyst. In contrast to platinum a significantly different hydrophobic behavior of the RuSe/C catalysts is found. Low open circuit voltage values measured for RuSe/C indicate an effect on both electrodes. The anode reaction was also influenced by the different cathode catalysts. As a result of the formation of H2O2 at the cathode, which passes through the membrane from cathode to anode side, a mixed anode potential is formed. By comparing RuSe/C catalysts before and after electrochemical stressing, changes of the catalysts are determined. Postmortem surface analysis (by X-ray photoelectron spectroscopy) revealed that catalyst composition and MEA structure changed during electrochemical stressing. During fuel cell operation selenium oxide is removed from the surface of the catalysts to a large extent. Additionally, a segregation effect of selenium in RuSe to the surface is identified.