Covert shifts of attention are usually reflected in RT differences between responses to valid and invalid cues in the Posner spatial attention task. Such inferences about covert shifts of attention do not control for microsaccades in the cue-target interval. We analyzed the effects of microsaccade orientation on RTs in four conditions, crossing peripheral visual and auditory cues with peripheral visual and auditory discrimination targets. Reaction time was generally faster on trials without microsaccades in the cue-target interval. If microsaccades occurred, the target-location congruency of the last microsaccade in the cue-target interval interacted in a complex way with cue validity. For valid visual cues, irrespective of whether the discrimination target was visual or auditory, target-congruent microsaccades delayed RT. For invalid cues, target-incongruent microsaccades facilitated RTs for visual target discrimination but delayed RT for auditory target discrimination. No reliable effects on RT were associated with auditory cues or with the first microsaccade in the cue-target interval. We discuss theoretical implications on the relation about spatial attention and oculomotor processes.