An illumination system of a microlithographic projection exposure apparatus has a pupil surface and an essentially flat arrangement of desirably individually drivable beam deviating elements for variable illumination of the pupil surface. Each beam deviating element allows deviation of a projection light beam incident on it to be achieved as a function of a control signal applied to the beam deviating element. A measurement illumination instrument directs a measurement light beam, independent of the projection light beams, onto a beam deviating element. A detector instrument records the measurement light beam after deviation by the beam deviating element. An evaluation unit determines the deviation of the projection light beam from measurement signals provided by the detector instrument.