Pupil size not only varies to changes in illumination but is also modulated by several cognitive factors, making it a potentially versatile physiological marker of cortical states. We recorded pupil dynamics while subjects continuously reported their bistable perception of ambiguous moving stimuli, plaids, and partially occluded rotating diamonds. We observed small (about 5% of surface change on average) but reliable pupil dilation around (-300 ms to 1.5 s) the button presses indicating the changes of percepts. We found that 70% of pupil dilation could be accounted for by the motor response. The remaining perceptual component was similar for spontaneously occurring transitions and transitions triggered by physical stimulus manipulations. Moreover, the amplitude of pupil modulation in the spontaneous condition was unrelated to the duration of each perceptual state. It is therefore unlikely that the mechanisms of endogenous perceptual bistability reflect in the pupil. In addition, we measured a clear constriction of the pupil after blinks (about 8% of surface change on average). As pupil changes have the potential to entail retino-cortical activity, their monitoring in studies of visual processing could prove worthwhile.