In this paper the modelling and optimization of a class of flexible assembly system is considered. The pipeline assembly systems are introduced, and the problem of throughput maximization is approached by a nested two-steps optimization procedure, carried on by means of a local search algorithm. The application analyzed concerns the maximization of the ratio between the throughput and the cost of a system for the assembly of cash registers. The production system is formed by one or more independent cells. For each type of cell architecture, the operations-to-robots assignment and the synchronization of the units to be assembled are optimized. The solution has been verified via simulation on the basis of a Petri-net representation of the assembly system.