Pt-Ru electrocatalysts are commonly applied anode materials for low-temperature fuel cells, as the addition of ruthenium improves the CO tolerance of the otherwise CO-sensitive platinum catalysts, either by an electronic effect or by electro-oxidation via oxygen-containing adsorbates in the so-called bifunctional mechanism. However, since bulk ruthenium oxidation already takes place at potentials of less than 1.0V vs. RHE and hydrous ruthenium oxide is suggested to be the active species in the bifunctional mechanism, the amount and specific nature of ruthenium oxides play an important role in fuel cell catalysis. Two Pt-Ru catalyst systems with distinctly different Pt-Ru separation have been studied: a carbon-supported Pt-Ru alloy electrocatalyst (Pt-Ru) and a mixture of carbon-supported Pt and carbon-supported Ru (Pt/Ru). Controlled heat-treatment experiments were carried out in air atmosphere at 100°C and 500°C to study the effect of deliberate ruthenium oxidation on the catalyst structure and electrochemical performance. At a heat-treatment temperature of 100°C, the Pt-Ru alloy appears less sensitive towards oxidation than the Pt/Ru mixture, although its lattice parameter increases from about 3.880Å to 3.907Å indicating that part of the ruthenium is pulled out of the alloy phase to form a (amorphous) ruthenium oxide. After heat-treatment at 500°C in air, X-ray patterns of the Pt-Ru alloy and the Pt/Ru mixture look almost alike. However, transmission electron micrographs reveal a distinctly different separation between the Pt and the Ru oxide phase with the Pt-Ru alloy system having many more Pt/Ru neighbour sites available. Complementary XPS measurements show a higher share of electrocatalytically inactive ruthenium oxide in the Pt/Ru mixture catalyst heat-treated at 100°C. The onset of the methanol oxidation reaction (MOR) for the different catalysts increases in the order Pt-Ru < Pt/Ru < Pt independent of the treatment underlining the importance of Pt/Ru site distribution and ruthenium oxide content for the electrocatalytic activity.