Previous electrophysiological studies have clearly identified separable neural events underlying early and late components of response anticipation. Functional neuroimaging studies, however, have so far failed to account for this separation. Here, we performed functional magnetic resonance imaging (fMRI) of an anticipation paradigm in 12 healthy adult subjects that reliably produced early and late expectancy waves in the electroencephalogram. We furthermore compared fMRI activations elicited during early and late anticipation to those associated with response conflict. Our results demonstrate the existence of distinct cortical and subcortical brain regions underlying early and late anticipation. Although late anticipatory behavior was associated with activations in dorsal ACC, frontal cortex, and thalamus, brain responses linked to the early expectancy wave were localized mainly in motor and premotor cortical areas as well as the caudate nucleus. Additionally, late anticipation was associated with increased activity in midbrain dopaminergic nuclei, very likely corresponding to the substantia nigra. Furthermore, whereas regions involved in late anticipation proved to be very similar to activations elicited by response conflict, this was not the case for early anticipation. The current study supports a distinction between early and late anticipatory processes, in line with a plethora of neurophysiological work, and for the first time describes the brain structures differentially involved in these processes.