High resolution solar absorption Fourier transform spectrometry (FTS) is the most precise ground-based remote sensing technique to measure the total column of atmospheric carbon dioxide. For carbon cycle studies as well as for the calibration and validation of spaceborne sensors the instrumental comparability of FTS systems is of critical importance. Retrievals from colocated measurements by two identically constructed FTS systems have been compared for the first time. Under clear sky conditions a precision for the retrieved xCO2 better than ∼0.1% is demonstrated and the instruments agree within ∼0.07%. An important factor in achieving such good comparability of the xCO2 is an accurate sampling of the internal reference laser. A periodic laser mis-sampling leads to ghosts (artificial spectral lines), which are mirrored images from original spectral lines. These ghosts can interfere with the spectral range of interest. The influence of the laser mis-sampling on the retrieved xCO2 and xO2 in the near-IR has been quantified. For a typical misalignment, the ratio of the ghost intensity compared to the intensity of the original spectral line is about 0.18% and in this case the retrieved xCO2 is wrong by 0.26% (1 ppm) and the retrieved xO2 is wrong by 0.2%.