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Reliability analysis of complex systems is a critical issue in reliability engineering. Motivated by practical needs, this paper investigates a Bayesian approach for system reliability assessment and prediction with multilevel heterogeneous data sets. Two major imperatives have been handled in the proposed approach, which provides a comprehensive Bayesian framework for the integration of multilevel heterogeneous data sets. In particular, the pass-fail data, lifetime data, and degradation data at different system levels are combined coherently for system reliability analysis. This approach goes beyond the alternatives that deal with solely multilevel pass-fail or lifetime data, and presents a more practical tool for real engineering applications. In addition, the indices for reliability assessment and prediction are constructed coherently within the proposed Bayesian framework. It gives rise to a natural manner of incorporating this approach into a decision-making procedure for system operation and management. The effectiveness of the proposed approach is illustrated with reliability analysis of a navigation satellite.