Accounting for load uncertainties plays an important role in the design of safe structural components of aircrafts under damage tolerance requirements. The purpose of this paper is to develop a reliability assessment technique for cracked structures submitted to non-stationary random fatigue loads modeled by first-order Markov chains with discrete state space and identified from in-flight measurements. The strategy based on a multi-level version of the cross-entropy method consists in progressively updating the tran- sition probability matrix in order to generate load sequences of increasing severity which are likely to cause failure. The proposed method is applied to a cracked M(T) specimen under the defined random fatigue loads. Load cycle interactions and retardation effects are accounted for by means of the PREFFAS crack closure model. The efficiency of the proposed approach in terms of computational cost is clearly observed for rare failure events in comparison with direct Monte Carlo simulations. In addition to the failure probability estimate, the multi-level cross-entropy method provides the analyst with information on the most probable load sequences at failure.