Power systems are vulnerable to both natural and man-related threats. The resulting contingencies - either single or multiple - may lead to wide-spread blackouts. However, the probabilities of the different events span over a wide range, hence the associated risk may be quite diverse. To address these issues a probabilistic risk assessment methodology and tool were developed within the Seventh Framework Program project AFTER. The aim of this paper is to describe the tool and its novelties, with special emphasis on the possibility to select and rank the most dangerous contingencies on the basis of probabilistic models of different threats affecting power system state, and to evaluate the effects of several factors (renewable penetration, protections and operators' delay) on the risk of operating a power system. Application examples are presented on a model of a realistic power system.