Future changes in extreme multi-day precipitation will influence the probability of floods in the river Rhine basin. In this paper the spread of the changes projected by climate models at the end of this century (2081–2100) is studied for a 17-member ensemble of a single Global Climate Model (GCM) and results from the Coupled Model Intercomparison Project Phase 3 (CMIP3) ensemble. All climate models were driven by the IPCC SRES A1B emission scenario. An analysis of variance model is formulated to disentangle the contributions from systematic differences between GCMs and internal climate variability. Both the changes in the mean and characteristics of extremes are considered. To estimate variances due to internal climate variability a bootstrap method was used. The changes from the GCM simulations were linked to the local scale using an advanced non-linear delta change approach. This approach uses climate responses of the GCM to transform the daily precipitation of 134 sub-basins of the river Rhine. The transformed precipitation series was used as input for the hydrological Hydrologiska Byråns Vattenbalansavdelning model to simulate future river discharges. Internal climate variability accounts for about 30 % of the total variance in the projected climate trends of average winter precipitation in the CMIP3 ensemble and explains a larger fraction of the total variance in the projected climate trends of extreme precipitation in the winter half-year. There is a good correspondence between the direction and spread of the changes in the return levels of extreme river discharges and extreme 10-day precipitation over the Rhine basin. This suggests that also for extreme discharges a large fraction of the total variance can be attributed to internal climate variability.