Axonal and dendritic integrity is affected early in Alzheimer's disease (AD). Studies using region of interest or voxel-based analysis of diffusion tensor imaging data found significant decline of fractional anisotropy, a marker of fiber tract integrity, in selected white matter areas. We applied a multivariate network analysis based on principal component analysis to fractional anisotropy maps derived from diffusion-weighted scans from 15 AD patients, and 14 elderly healthy controls. Fractional anisotropy maps were obtained from an EPI diffusion sequence using parallel imaging to reduce distortion artifacts. We used high-dimensional image warping to control for partial volume effects due to white matter atrophy in AD. We found a significant regional pattern of fiber changes (p<0.01) indicating that the integrity of intracortical projecting fiber tracts (including corpus callosum, cingulum and fornix, and frontal, temporal and occipital lobe white matter areas) was reduced, whereas extracortical projecting fiber tracts, including the pyramidal and extrapyramidal systems and somatosensory projections, were relatively preserved in AD. Effects of a univariate analysis were almost entirely contained within the multivariate effect. Our findings illustrate the use of a multivariate approach to fractional anisotropy data that takes advantage of the highly organized structure of anisotropy maps, and is independent of multiple comparison correction and partial volume effects. In agreement with post-mortem evidence, our study demonstrates dissociation between intracortical and extracortical projecting fiber systems in AD in the living human brain.