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We propose and analyze a method for computing failure probabilities of systems modeled as numerical deterministic models (e.g., PDEs) with uncertain input data. A failure occurs when a functional of the solution to the model is below (or above) some critical value. By combining recent results on quantile estimation and the multilevel Monte Carlo method, we develop a method that reduces computational cost without loss of accuracy. We show how the computational cost of the method relates to error tolerance of the failure probability. For a wide and common class of problems, the computational cost is asymptotically proportional to solving a single accurate realization of the numerical model, i.e., independent of the number of samples. Significant reductions in computational cost are also observed in numerical experiments.