Recent findings suggest white matter hyperintensities (WMH) that appear on FLAIR images may play a role in the evolution of Alzheimer’s disease (AD). Here, we developed a novel algorithm that simultaneously detects and locates WMH, based on a FLAIR atlas database and a multi-atlas fusion algorithm. The method showed a respectful WMH detection accuracy. We also investigated region-specific WMH load in participants for whom amyloid imaging and vascular data were available. The results suggested that posterior WMH is related to amyloid deposition; whereas anterior and parietal WMH is associated with vascular risk factors.