The flexible manufacturing system (FMS) has attracted substantial amount of research effort during the last twenty years. Most of the studies address the issues of flexibility, productivity, cost, and so forth. The impact of flexible lines on product quality is less studied. This paper intends to address this issue by applying a Markov model to evaluate quality performance of a flexible manufacturing system. Closed expressions to calculate good part probability are derived and discussions to maintain high product quality are carried out. An example of flexible fixture in machining system is provided to illustrate the applicability of the method. The results of this study suggest a possible approach to investigate the impact of flexibility on product quality and, finally, with extensions and enrichment of the model, may lead to provide production engineers and managers a better understanding of the quality implications and to summarize some general guidelines of operation management in flexible manufacturing systems.