Simulation and optimisation of supply chains are becoming increasingly important to obtain the best performance of a supply chain due to rapid changes in global markets. While simulation is very important for analysing of the existing system’s logic and its underlying laws, application of optimisation in supply chain management guarantees the best performance of the supply chain. Both are indispensable support tools for decision-making. Though much work has been done in applying mathematical optimisation methods to real world problems, there are still many unresolved issues in the optimisation of large and complex real world logistic systems. The paper will give a survey along the following main lines: sources of uncertainty in logistics at all three levels: strategic, tactical, operational, definitions of reliability and robustness of logistics systems, synergy between optimisation and simulation of supply chains, and techniques for supply chain optimisation