It has recently been demonstrated that the presentation of a rare target in a visual oddball paradigm induces a prolonged inhibition of microsaccades. In the field of electrophysiology, the amplitude of the P300 component in event-related potentials (ERP) has been shown to be sensitive to the stimulus category (target vs. non target) of the eliciting stimulus, its overall probability, and the preceding stimulus sequence. In the present study we further specify the functional underpinnings of the prolonged microsaccadic inhibition in the visual oddball task, showing that the stimulus category, the frequency of a stimulus and the preceding stimulus sequence influence microsaccade rate. Furthermore, by co-recording ERPs and eye-movements, we were able to demonstrate that, despite being largely sensitive to the same experimental manipulation, the amplitude of P300 and the microsaccadic inhibition predict each other very weakly, and thus constitute two independent measures of the brain’s response to rare targets in the visual oddball paradigm.