We compared and analyzed data of vertically Integrated Water Vapor (IWV) from two different re-analysis models (The comparison was performed taking into account the geopotential height differences between each GNSS station and 5 the correspondent values assigned by the models. Thus, the set of GNSS stations was divided into 3 groups: Small, Large and Critical height difference stations. Moreover, the performance of the re-analysis models was also analyzed by using an additional classification of three levels according to the mean IWV (IW V ) value expected at the station: IW V > 30 kg m −2 , 12 kg m −2 IW V 30 kg m −2 and IW V < 12 kg m −2 .Both models (IW V ERA−Interim and IW V M ERRA−2 ) offered a very good representation of the IWV from GNSS values 10 (IW V GN SS ) for stations with a Small height difference (smaller than 100 meters). That is to say, the differences between the mean values of IWV from GNSS (IW V GN SS ) with respect to the IWV averages from both re-analysis models are always below 7 % of the IW V GN SS in the worse case.In general, the discrepancies between the re-analysis models with respect to IW V GN SS raise as the geopotential height difference between the GNSS station and the static geopotential height interpolated from the models grows. Effectively, the 15 difference between IW V GN SS and IWV from the re-analysis models can be as large as 10 kg m −2 for stations with a critical height difference (larger than 500 meters). For this reason, we proposed a numerical correction that compensates the effect of the geopotential height difference and the results were tested with values from ERA-Interim.The suggested correction was successful and reduces the differences |IW V GN SS − IW V ERA−Interim | to less than a 7 % of the mean IW V GN SS values. This strategy is especially recommended for stations that were classified as Critical, most of 20 them located in mountainous areas of South America. In the case of Large height difference stations, the correction procedure is not advisable either for a coastal station and/or stations in islands. Generally in those cases, two or more grid point are on the water. Thus, the interpolated IWV value for the re-analysis model will be overestimated. At one hand, if the geopotential height of the model is smaller than the geopotential height of the GNSS station, the subtracting numerical correction would compensate this overestimation of IWV near the water and thus the strategy will represent an improvement. On the other 25 Water vapor is an abundant natural greenhouse gas of the atmosphere. The knowledge of its variability in time and space is very important to understand the global climate system (Dessler et al., 2008). Most of the regional comparisons of IWV from GNSS are aimed at validating the technique by comparing with radiosonde and radiometers where available. A complete example of this is the work of Van Malderen et al. (2014) who compared IWV GPS (Global Positioning System) with IWV derived from ground-based sun photometers, radiosondes and satel...