In a control system for an internal combustion engine, a control unit controls a throttle valve provided in an intake pipe and/or an on-off valve provided in an exhaust gas recirculation pipe when an ignition switch is turned on, in such a manner that an opening degree of the throttle valve and/or an opening degree of the on-off valve is made to be larger than that of a condition before the ignition switch is turned on. In the above Ig-on control, in which the throttle valve and/or the on-off valve is largely opened, a piston is reciprocated in order that gas in a combustion chamber is discharged to an outside of the combustion chamber.