In a visual oddball task the presentation of rare targets induces a prolonged microsaccadic inhibition as compared to standards. Here, we replicated this effect also in the auditory modality. In addition, although auditory standards induced a more limited modulation of microsaccadic frequency as compared to visual standards, auditory oddballs induced a prolonged microsaccadic inhibition. With bimodal standard stimuli the microsaccadic response was determined by the attended modality, resembling that produced by attended unimodal stimuli. The present findings support the idea that the microsaccadic response to oddball and standard stimuli is partly driven by cognitive mechanisms common to both the visual and the auditory modality, and that microsaccades can be used as an implicit behavioral measure of ongoing cognitive processes.