In this study we have attempted to define the neural circuits differentially activated by cognitive interference. We used event-related functional magnetic resonance imaging (fMRI) to identify areas of the brain that are activated by the Stroop word-color task in two experiments. In the first experiment, we used infrequent, incongruent colored word stimuli to elicit strong Stroop interference (the ‘conventional Stroop’ paradigm). In the second experiment, we used infrequent, congruent colored words (the ‘inverse Stroop’ paradigm) to confirm that the regions identified in the first experiment were in fact specifically related to the Stroop effect and not to nonspecific oddball effects associated with the use of infrequent stimuli. Performance of the conventional Stroop specifically activated the anterior cingulate, insula, premotor and inferior frontal regions. These activated regions in the current experiment are consistent with those activated in fMRI experiments that use a more traditional block design. Finally, analysis of the time course of fMRI signal changes demonstrated differential onset and offset of signal changes in these activated regions. The time course results suggest that the action of various brain areas can be temporally dissociated.