This book proposes a novel design method that combines both genetic programming (GP) to automatically explore the open-ended design space and bond graphs (BG) to unify design representations of multi-domain Mechatronic systems. Results show that the method, formally called GPBG method, can successfully design analogue filters, vibration absorbers, micro-electro-mechanical systems, and vehicle suspension systems, all in an automatic or semi-automatic way. It also investigates the very important issue of co-designing body-structures and dynamic controllers in automated design of Mechatronic systems.