Abstract. An Atmospheric Monitoring System (AMS) is mandatory and a key element of a space-based mission which aims to detect Ultra-High Energy Cosmic Rays (UHECR). JEM-EUSO has a dedicated atmospheric monitoring system that plays a fundamental role in our understanding of the atmospheric conditions in the Field of View (FoV) of the telescope. Our AMS consists of an infrared camera and a LIDAR device that are being fully designed with space qualification to fulfil the scientific requirements of this space mission. This AMS will provide information of the cloud cover in the FoV of JEM-EUSO, as well as measurements of the cloud top altitudes with an accuracy of 500 m and the optical depth profile of the atmosphere transmittance in the direction of each air shower with an accuracy of 0.15 degree and a resolution of 500 m. This will ensure that the energy of the primary UHECR and the depth of maximum development of the EAS (Extensive Air Shower) are measured with an accuracy better than 30% and 120 g/cm 2 , for EAS occurring either in the clear sky or with the EAS depth of maximum development above optically thick cloud layers. Moreover novel stereoscopic and radiometric retrieval techniques are under development to infer the Cloud Top Height (CTH) from the brightness temperature patterns obtained from the infrared camera. is compared to that of clear sky signal (green line). Now the fluorescence radiation suffers absorption but the Cherenkov peak takes place on ground due to the fact that the cirrus clouds are thin clouds.