Marked increases of CO2, H2 and He dissolved in thermal waters and changes in the dissolved carbon isotopic composition, were observed at Stromboli before the 28 December 2002 eruption and before a violent explosive paroxysm occurred on 5 April 2003. High anomalous CO2 flux values were recorded at the crater rim since a week before the eruption onset. The first anomalies in the thermal waters (dissolved CO2 amount) appeared some months before the eruption, when magma column rose at a very high level in the conduit. High peaks of dissolved H2 and He were recorded a few days before the paroxysm. Carbon isotopic composition indicates a magmatic origin of the dissolved CO2 whose increase, together with those of H2 and He, is attributed to an increasing output of deep gases likely produced by depressurization of a rising batch of a deep gas-rich magma, whose fragments have been emitted during the explosion.