This chapter addresses the resolution of scheduling in manufacturing systems subject to perturbations. The planning of Manufacturing Systems involves frequently the resolution of a huge amount and variety of combinatorial optimisation problems with an important impact on the performance of manufacturing organisations. Examples of those problems are the sequencing and scheduling problems in manufacturing management, routing and transportation, layout design and timetabling problems. New organizational and technological paradigms are needed to reply to the modern manufacturing systems challenges. The traditional structure of manufacturing industries is constructed upon the three pillars of land, labour and capital. The challenge is to move towards a new structure, which can be described as innovating manufacturing, founded on knowledge and capital. Future manufacturing solutions must identify multiple perspectives and linkages between novel approaches to customization, customer response, logistics and maintenance. The current typically linear approach to research, development, design, construction and assembly will be replaced by simultaneous activity in all areas to satisfying global demand and shorten time-to-market (MANUFUTURE, 2004). Multi-agent paradigm is emerging for the development of solutions to very hard distributed computational problems. This paradigm is based either on the activity of "intelligent" agents which perform complex functionalities or on the exploitation of a large number of simple agents that can produce an overall intelligent behaviour leading to the solution of alleged almost intractable problems. The multi-agent paradigm is often inspired by biological systems. Meta-Heuristics (MH) form a class of powerful and practical solution techniques for tackling complex, large-scale combinatorial problems producing efficiently high-quality solutions. From the literature we can conclude that they are adequate for static problems. However, real scheduling problems are quite dynamic, considering the arrival of new orders, orders being cancelled, machine delays or faults, etc. Scheduling problem in dynamic environments have been investigated by a number of authors, see for example (Aytug et al.,