The JEM-EUSO (Japanese Experiment Module-Extreme Universe Space Observatory) telescope will measure Ultra High Energy Cosmic Ray properties by detecting the UV fluorescence light generated in the interaction between cosmic rays and the atmosphere. Therefore, information on the state of clouds in the atmosphere is crucial for a proper interpretation of the data. For a real-time observation of the clouds in the telescope Field of View (FoV), JEM-EUSO will use an atmospheric monitoring system composed of a Lidar (LIght Detection And Ranging) and an Infra-Red Camera. In this article the focus is on the IR camera data. To retrieve the Cloud Top Height (CTH) from IR images, three different methods are considered here. The first one is based on bi-spectral stereo vision algorithms and requires two different views of the same scene in different spectral bands. For the second one, brightness temperatures provided by the IR camera are converted to effective cloud top temperatures, from which the CTH is estimated using the vertical temperature profiles. A third method that uses primary Numerical Weather Prediction (NWP) model output parameters, such as the cloud fraction, has also been considered to retrieve the CTH. This article presents a first analysis, in which the heights retrieved by these three methodologies are compared with the heights given by MODIS (MODerate resolution Imaging Spectroradiometer) sensor installed on the polar satellite Terra. Since all these methods are suitable for the JEM-EUSO mission, they could be used in the future in a complementary way to improve the accuracy of the CTH retrieval.