An advanced control system for the optimal operation and management of autonomous wind-diesel systems is presented. This system minimises the production costs through an on-line optimal scheduling of the power units, which takes into account the technical constraints of the diesel units, as well as short-term forecasts of the load and renewable resources. The power system security is maximised through on-line security assessment modules, which enable the power system to withstand sudden changes in the production of the renewable sources. The control system was evaluated using data from the island of Lemnos, where it has been installed and operated since January 1995.