A method of operating an internal combustion engine having an; electromagnetically driven intake valves for a vehicle. With the method, deviation of an opening operation of the electromagnetically driven intake valve in response to a command signal for opening the intake valve from a predetermined characteristic is detected, and at least one of parameters used for controlling operation of the internal combustion engine is corrected so as to reduce a change in an intake air charging state in which the internal combustion engine is charge with the intake air. A valve closing timing of the intake valve or a valve closing timing of the exhaust valve that cooperates with the intake valve may be used as parameters to be corrected.