The interest in compound-specific isotope analysis for product authenticity control and source differentiation in environmental sciences has grown rapidly during the last decade. However, the isotopic analysis of very polar analytes is a challenging task due to the lack of suitable chromatographic separation techniques which can be used coupled to isotope ratio mass spectrometry. In this work, we present the first method to measure carbon isotope compositions of the widely applied herbicide glyphosate and its metabolite aminomethylphosphonic acid (AMPA) by liquid chromatography coupled to isotope ratio mass spectrometry. We demonstrate that this analysis can be carried out either in cation exchange or in reversed-phase separation modes. The reversed-phase separation yields a better performance in terms of resolution compared with the cation exchange method. The measurement of commercial glyphosate herbicide samples show its principal applicability and reveals a wide range of delta C-13 values between -24 and -34 aEuro degrees for different manufacturers. The absolute minimum amounts required to perform a precise and accurate determination of carbon isotope compositions of glyphosate and AMPA were in the sub-microgram range. The method proposed is sensitive enough to further perform the experiments that are necessary to better understand the carbon isotope fractionation associated to the natural degradation of glyphosate into AMPA. Furthermore, it can be used for contaminant source allocation and product authenticity as well.