The performance and the efficiency of direct methanol fuel cells (DMFCs) are affected by the methanol permeation from the anode to the cathode. A widely used method to measure the methanol permeation in a DMFC is the analysis of the carbon dioxide content of the cathode exhaust. During the operation of a DMFC large amounts of carbon dioxide are produced in the anodic catalyst layer which can diffuse partially to the cathode. As a consequence the carbon dioxide in the cathodic exhaust gas stream is expected to consist of two fractions: the carbon dioxide resulting from the oxidation of the permeating methanol and the carbon dioxide diffusing from the anode to the cathode. In this work we describe away to separate the distribution of the two fractions under real DMFC operating conditions. As a results we found that with low methanol concentrations (<1 M) and high current densities the amount of carbon dioxide passing from the anode to the cathode can even be higher than the amount of carbon dioxide formed at the cathode by methanol oxidation.