This book constitutes the refereed proceedings of the Third European Performance Engineering Workshop, EPEW 2006, held in Budapest, Hungary in June 2006. The 16 revised full papers presented were carefully reviewed and selected from 40 submissions. The papers are organized in topical sections on stochastic process algebra, workloads and benchmarks, theory of stochastic processes, formal dependability and performance evaluation, as well as queues, theory and practice.