This paper presents a methodology for evaluating the performance of Programmable Electronic Systems (PES) used for safety applications. The most common PESs used in the industry are identified. Markov modeling techniques are used to develop the reliability model. The major aspects of the analysis address the random hardware failures, the uncertainty associated with these failures, a methodology to propagate these uncertainties in the Markov model, and modeling of common cause failures. The elements of this methodology are applied to an example using a Triple Redundant PES without inter-processor communication. The performance of the PES is quantified in terms of its reliability, probability to fail safe, and probability to fail dangerous within a mission time. The effect of model input parameters (component failure rates, diagnostic coverage), their uncertainties and common cause failures on the performance of the PES is evaluated.