A variable valve control system for an internal combustion engine including a plurality of cylinders, the variable valve control system including a variable lift characteristic control mechanism to adjust a valve lift characteristic of each of intake valves. The variable valve control system is configured to perform determining an engine condition indicator in correlation with an actual relative variation in the valve lift characteristic between the cylinders; determining a desired valve lift characteristic in accordance with an operating condition of the internal combustion engine; controlling the valve lift characteristic of each of the intake valves in accordance with the desired valve lift characteristic; determining the engine condition indicator when the desired valve lift characteristic is equal to a predetermined small valve lift characteristic setting; and expanding the small valve lift characteristic setting if the determined engine condition indicator is larger than a predetermined first threshold value.