This Special issue (SI) of Applied Thermal Engineering presents fourteen selected contributions from the 13th Conference Process Integration, Modelling and Optimisation for Energy Saving and Pollution Reduction– PRES 2010. It benefits from the long-term cooperation between the PRES conferences and the journal. The selected papers cover important subjects: improved design of integrated energy systems and their optimal operation, Process Integration of biorefineries, Waste to Energy, advanced heat transfer enhancement, Fuel Cell applications for increased energy efficiency.