This study investigated the neurobiological basis of attentional control dysfunction in neurodegenerative disease by determining the effect of regional brain atrophy on Flanker task performance of neurodegenerative patients. We hypothesized that atrophy in DLPFC and ACC would be significantly associated with decreased attentional control performance on the Flanker task. We used voxel-based morphometry (VBM) to measure the relationship between MRI measures of regional grey matter atrophy and performance on a version of the Flanker task, measured by accuracy and response time. Sixty-five subjects participated, including patients with frontotemporal dementia, Alzheimer's disease, mild cognitive impairment, non-fluent progressive aphasia, corticobasal degeneration, progressive supranuclear palsy, semantic dementia, and healthy controls. Accuracy measures of attentional control and response time measures of attentional control were associated with two different patterns of regional atrophy across subjects. First, there was an association between left hemisphere DLPFC and ACC atrophy and poorer attentional control accuracy. Second, right hemisphere temporal-parietal junction (TPJ) and ventrolateral prefrontal cortex (VLPFC) and DLPFC atrophy were associated with slower response times during attentional control on accurate trials, which may reflect emergent involvement due to deficits in the DLPFC-ACC network.