A control system for an internal combustion engine that has at least one fuel injection valve for injecting fuel into a combustion chamber of the engine, and burns the injected fuel by compressing an air-fuel mixture in the combustion chamber. An operating condition of the engine and/or a refueling condition of a fuel tank for supplying fuel to the engine are/is detected. At least one operating parameter of the engine is changed when at least one of the engine operating condition and the refueling condition detected by the condition detecting means satisfies a predetermined condition in a predetermined low load operating condition of the engine. A cetane number of the fuel in use is estimated according to an ignition timing of the fuel detected after changing the at least one operating parameter of the engine.