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This paper evaluates the impact of transient errors in the operating system of a COTS-based system (CETIA board with two PowerPC 750 processors running LynxOS) and quantifies their effects at both the OS and at the application level. The study has been conducted using aSoftware-Implemented Fault Injection tool (Xception) and both realistic programs and synthetic workloads (to focus on specific OS features) have been used. The results provide a comprehensive picture of the impact of faults on LynxOS key features (process scheduling and the most frequent system calls), data integrity, error propagation, application termination, and correctness of application results.