White matter hyperintensities (WMHIs) visible on magnetic resonance imaging (MRI) are common in both healthy adults and in those with medical or psychiatric problems. A practical methodological issue for diffusion tensor imaging (DTI) researchers is whether to include, or exclude, participants from a control group who have WMHIs. The aim of this study was to compare the influence of WMHIs on whole-brain DTI in trauma control subjects. Participants were 48 patients (no-WMHIs, n=36; 2+WMHIs, n=12) prospectively recruited from the Emergency Department of Vancouver General Hospital (British Columbia, Canada). Participants completed an MRI brain scan at 6-8 weeks postinjury (mean, 47.3 days; standard deviation [SD], 6.2; range, 39-66). DTI was used to examine the integrity of white matter (WM) in 50 regions of the brain using measures of fractional anisotropy (FA), and mean (MD), radial (RD), and axial (AD) diffusivity. FA values that were >2 SDs below the mean, and MD, RD, and AD values that were >2 SDs above the mean, were classified as "abnormal scores" indicative of reduced WM integrity. In the entire sample, the 2+WMHI group had a greater number of abnormal FA, MD, and RD scores, compared to the no-WMHI group (p<0.015 and Cohen's d >0.82, indicating large to very large effect sizes, for all comparisons). When controlling for the effects of age using a matched-groups design, the 2+WMHI group still had a significantly greater number of abnormal FA, MD, and RD scores, compared to the no-WMHI group (all p<0.012, all d >0.89, large to very large effect sizes). Researchers should be aware that the inclusion or exclusion of subjects with incidental WMHIs will influence the results of DTI studies.