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Embedded operating systems are becoming widely used in electronic systems for fields ranging from the mobile phone to the industrial control mechanisms. The major advantages in using embedded operating systems include the capability of adapting the electronic functionalities to several kind of applications while respecting the real-time constraints. These characteristics make them attractive also for specific fields where the dependability is a major concern, such as automotive, avionic or space missions. When the dependability is considered embedded operating systems must guarantee their functionality under the presence of Single Event Upsets (SEUs) that may alter their modules. In this paper we proposed a novel methodology for the analysis and the classification of SEU's induced effects that may corrupt the functionality of an embedded operating system while executing a real-time application. The developed method is based on a fault injection engine that is able to inject and classify SEU within the internal registers and memory cells of an embedded operating systems running on a FPGA device. As case study we evaluated the muC-Linux operating system running on a Xilinx-based microprocessor core supported by a Virtex-II Pro SRAM-based FPGA. Experimental results are presented and commented.