Fixational eye movements occur involuntarily during visual fixation of stationary scenes. The fastest components of these miniature eye movements are microsaccades, which can be observed about once per second. Recent studies demonstrated that microsaccades are linked to covert shifts of visual attention. Here, we generalized this finding in two ways. First, we used peripheral cues, rather than the centrally presented cues of earlier studies. Second, we spatially cued attention in vision and audition to visual and auditory targets. An analysis of microsaccade responses revealed an equivalent impact of visual and auditory cues on microsaccade-rate signature (i.e. an initial inhibition followed by an overshoot and a final return to the pre-cue baseline rate). With visual cues or visual targets, microsaccades were briefly aligned with cue direction and then opposite to cue direction during the overshoot epoch, probably as a result of an inhibition of an automatic saccade to the peripheral cue. With left auditory cues and auditory targets microsaccades oriented in cue direction. We argue that microsaccades can be used to study crossmodal integration of sensory information and to map the time course of saccade preparation during covert shifts of visual and auditory attention.