Abstract. Within the Global Climate Observing System (GCOS) Reference Upper Air Network (GRUAN) there is a need for an assessment of the uncertainty in the Integrated Water Vapour (IWV) in the atmosphere estimated from ground-based GNSS observations. All relevant error sources in GNSS-derived IWV is therefore essential to be investigated. We present two approaches, a statistical and a theoretical analysis, for the assessment of the uncertainty of the IWV. It will be implemented to the GNSS IWV data stream for GRUAN in order to obtain a specific uncertainty for each data point. In addition, specific recommendations are made to GRUAN on hardware, software, and data processing practices to minimize the IWV uncertainty. By combining the uncertainties associated with the input variables in the estimations of the IWV, we calculated the IWV uncertainties for several GRUAN sites with different weather conditions. The results show a similar relative importance of all uncertainty contributions where the uncertainties in the Zenith Total Delay (ZTD) dominate the error budget of the IWV contributing with over 75 % to the total IWV uncertainty. The impact of the uncertainty associated with the conversion factor between the IWV and the Zenith Wet Delay (ZWD) is proportional to the amount of water vapour and increases slightly for moist weather conditions. The GRUAN GNSS IWV uncertainty data will provide a quantified confidence to be used for the validation of other measurement techniques, taking the uncertainty into account from diurnal to decadal time scales.