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During the Pleistocene the vegetation changes in the high Colombian Andes included changes from C3 to C4 plants. This is inferred from ?13C values of the C31 n-alkane from the Funza-2 sedimentary record taken from the high plain of Bogotá at 2550 m elevation. The environmental factors thought to be responsible for these changes were investigated using a single point simulation of the BIOME3 vegetation model, including changes in precipitation, temperature and atmospheric CO2 concentrations. The model shows that changes are for a major part caused by these latter two factors. The isotopic signature of the n-alkanes of several extant C3 and C4 grasses from the area were determined to calibrate the interpretation of the isotopic record. From the geochemical record, we estimated the altitudinal distribution of C3 and C4 plants, using present grass distribution patterns based on floristic data as a template. This information, in combination with palaeotemperature estimates, enabled the reconstruction of atmospheric CO2 concentrations. The reconstructed CO2 concentrations follow the trends of the Vostok Antarctic ice core through three glacial and two interglacial stages. The lowest calculated CO2 concentration is ca. 210 ppmV for the glacial maxima and within the range of lowest values from Vostok, our highest value (310 ppmV) is for interglacial MIS 7. This represents a new method to reconstruct palaeoatmospheric pCO2. It is less accurate than measurements from ice cores, but has potential to be used for sediments that are much older than the ice cores.