Current strategic and technological trends in discrete-part manufacturing require extensive and exible automation of the underlying production systems. However, even though a great deal of work has been done to facilitate manufacturing automation at the hardware component level, currently there is no adequately developed control methodology for these environments. In particular, it has recently been realized by the manufacturing community that any successful attempt towards the extensive automation of these environments requires the establishment o f logically correct and robust behavior from the underlying system. The resulting line of research is complementary to the most traditional performance-oriented control, and it has come to be known as the structural control of the contemporary exibly automated production environment. In this chapter, we initially discuss the role of structural control in the broader context of realtime control of exible manufacturing systems FMS, and in continuation, we present the major results of our research program on manufacturing system deadlock, currently the predominant structural control problem in the manufacturing research literature. In the concluding section, we also indicate how these results should be integrated in contemporary FMS controllers, and highlight directions for future research in the FMS structural control area.