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This paper presents the application of a framework for reliability analysis of substation automation (SA) system functions. The framework is based on probabilistic relational models which combines probabilistic reasoning offered by Bayesian networks together with architecture models in form of entity relationship diagrams. In the analysis, both the physical infrastructure, and the logical structure of the system, is regarded in terms of qualitative modeling and quantitative analysis. Moreover, the framework treats the aspect of failures caused by software. An example is detailed with the framework applied to an IEC 61850-based SA system. The logical structure, including functions and their relations, is modeled in accordance with Pieces of Information for COMmunication (PICOM) defined in the IEC 61850 standard. By applying PICOMs as frame of reference when modeling functions the model instantiation becomes more standardized compared to subjectively defining functions. A quantitative reliability analysis is performed on a function for tipping a circuit breaker in case of mismatch between currents. The result is presented both in terms of a qualitative architecture model and a quantitative result showing the probability of successful operation during a period of one year.