The EU Mine Waste Directive (MWD) requires the risk-based inventory of all mine waste sites in Europe by 2012. Major incidents involving mine waste facilities in the historic mining areas in the Carpathian Basin and the associated environmental risks have triggered the development of new EU environmental legislation to prevent and minimize the effects of such incidents. In order to address the mining environmental problems a standard risk-based pre-selection protocol has been developed by the EU Commission. This paper evaluates the protocol by applying it to real-life cases and carrying out uncertainty analysis. All together 145 ore mine waste sites have been selected for scientific testing and evaluation using the EU Pre-selection Protocol as a case study from Hungary. Key parameters such as the topographic slope and distance to the nearest surface and groundwater bodies, to settlements and protected areas are calculated and statistically evaluated in order to calibrate the risk assessment models to local conditions. According to the results, out of the 145 sites, 11 waste sites are the most risky with topographic slope >20o, 57 sites are within distance less than 500m to the nearest surface water bodies (streams and lakes), and 33 sites are within distance less than 680m to the nearest settlements. Moreover, 25 sites are located directly above the groundwater bodies with 'poor status' and 91 sites are located inside the protected Natura 2000 areas. According to the number of YES responses of the Pre-selection Protocol, a relative risk-based site ranking was performed using STATGRAPHICS® statistical software which resulted in 127 sites are directed to 'Examine Further' using EU thresholds and 129 sites directed to 'Examine Further' using local median-based thresholds. In addition to, 16 sites without pathway (based on EU thresholds) and 18 sites (based on the local thresholds) are directed to 'No Need to Examine Further'. Similar study is being carried out in Turkey with EU support under the accession process to provide inventory of the Turkish mine waste sites.