An engine with EGR system equipped with a variable geometry turbocharger and a particulate filter is provided in which the nozzle angle (nozzle area) of the variable geometry turbocharger can be controlled accurately and by a simple means in accordance with the change in the internal EGR rate due to deposition of particulate matter in the particulate filter, and the effect of EGR to reduce NOx emission is obtained in the whole operation range of the engine without deteriorating durability of the engine.