The interaction of quantity and quality performance in a factory is clearly of great economic importance. However, there is very little quantitative analytical literature in this area. This thesis is an essential early research step in analyzing how production system design, quality, and productivity are inter-related in transfer lines. We develop a new Markov process model for machines with both quality and operational failures, and we identify important differences between types of quality failures. We present analytic models, solution techniques, performance evaluations, and validation of twomachine systems as well as longer transfer lines. Through numerical studies, we have investigated some of the conventional wisdom on this interaction, and we have found that the wisdom holds only under specific conditions, and we show that the conventional wisdom is wrong under other conditions. We therefore anticipate that more such research will have a dramatic effect on the performance of factories, and we propose promising research directions.