This study evaluates the capability of atmospheric CO<sub>2</sub> column measurements under cloudy conditions using an airborne intensity-modulated continuous-wave integrated-path-differential-absorption lidar operating in the 1.57-μm CO<sub>2</sub> absorption band. The atmospheric CO<sub>2</sub> column amounts from the aircraft to the tops of optically thick cumulus clouds and to the surface in the presence of optically thin clouds are retrieved from lidar data obtained during the summer 2011 and spring 2013 flight campaigns, respectively. For the case of intervening thin cirrus clouds with an average cloud optical depth of about 0.16 over an arid/semi-arid area, the CO<sub>2</sub> column measurements from 12.2 km altitude were found to be consistent with the cloud free conditions with a lower precision due to the additional optical attenuation of the thin clouds. The clear sky precision for this flight campaign case was about 0.72% for a 0.1-s integration, which was close to previously reported flight campaign results. For a vegetated area and lidar path lengths of 8 to 12 km, the precision of the measured differential absorption optical depths to the surface was 1.3 - 2.2% for 0.1-s integration. The precision of the CO<sub>2</sub> column measurements to thick clouds with reflectance about 1/10 of that of the surface was about a factor of 2 to 3 lower than that to the surface owing to weaker lidar returns from clouds and a smaller CO<sub>2</sub> differential absorption optical depth compared to that for the entire column.