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The paper deals with development of the probabilistic approach to the assessment of risk due to lightning flashes striking smart buildings. Overvoltages resulting from flashes direct or near the building and the incoming lines are considered as well as the effect of direct coupling of the lightning electromagnetic field (LEMP) on equipment and devices of building automation systems. Special attention is devoted to the probability of systems failure and on the way to evaluate the influence of different protection measures in reducing such probability. The most critical points of the system and the optimal selection, installation and coordination of protection means are discussed in order to reduce the risk to a tolerable level.