► A ceilometer was used to probe the atmosphere above the TeV instrument H.E.S.S. ► The atmosphere was modelled using MODTRAN and used in cosmic-ray simulations. ► Cosmic-ray simulations were matched to real background data. ► TeV Gamma-ray data affected by poor weather was successfully corrected. The current generation of imaging atmospheric Cherenkov telescopes are allowing the sky to be probed with greater sensitivity than ever before in the energy range around and above 100 GeV. To minimise the systematic errors on derived fluxes a full calibration of the atmospheric properties is important given the calorimetric nature of the technique. In this paper we discuss an approach to address this problem by using a ceilometer co-pointed with the H.E.S.S. telescopes and present the results of the application of this method to a set of observational data taken on the active galactic nucleus (AGN) PKS 2155-304 in 2004.