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In many flexible manufacturing systems, batch production is often adopted to improve product quality. For example, in automotive paint shops, vehicles with same colors are typically grouped into small batches to reduce quality degradation and purge cost due to color change. In this paper, we present an analytical method to evaluate the quality performance of flexible manufacturing systems with batch operations. In addition, we investigate the impact of product sequencing and batch policies on product quality and present some insights to achieve better quality using these policies.