Abstract. Stratospheric intrusion (SI) events are a topic of ongoing research, especially because of their ability to change the oxidation capacity of the troposphere and their contribution to tropospheric ozone levels. In this work, a novel tool called STEFLUX (Stratosphere-to-Troposphere Exchange Flux) is presented, discussed, and used to provide a first long-term investigation of SI over two global hot-spot regions for climate change and air pollution: the southern Himalayas and the central Mediterranean Basin. The main purpose of STEFLUX is to obtain a fast-computing and reliable identification of the SI events occurring at a specific location and during a specified time window. It relies on a compiled stratosphere-to-troposphere exchange (STE) climatology, which makes use of the ERA-Interim reanalysis dataset from the ECMWF, as well as a refined version of a well-established Lagrangian methodology. STEFLUX results are compared to the SI observations (SIO) at two high-mountain WMO/GAW global stations in these climate hot spots, i.e., the Nepal Climate Observatory-Pyramid (NCO-P, 5079 m a.s.l.) and Mt. Cimone (2165 m a.s.l.), which are often affected by SI events. Compared to the observational datasets at the two specific measurement sites, STEFLUX is able to detect SI events on a regional scale. Furthermore, it has the advantage of retaining additional information concerning the pathway of stratospheric-affected air masses, such as the location of tropopause crossing and other meteorological parameters along the trajectories. However, STEFLUX neglects mixing and dilution that air masses undergo along their transport within the troposphere. Therefore, the regional-scale STEFLUX events cannot be expected to perfectly reproduce the point measurements at NCO-P and Mt. Cimone, which are also affected by small-scale (orographic) circulations. Still, the seasonal variability in SI events according to SIO and STEFLUX agrees fairly well. By exploiting the fact that the ERA-Interim reanalysis extends back to 1979, the long-term climatology of SI events at NCO-P and Mt. Cimone is also assessed in this work. The analysis of the 35-year record at both stations denies the existence of any significant trend in the SI frequency, except for winter seasons at NCO-P. Furthermore, for the first time, by using the STEFLUX outputs, we investigate the potential impact of specific climate factors (i.e. ENSO, QBO, and solar activity) on SI frequency variability over the Mediterranean Basin and the Himalayas.