Diffusion tensor imaging (DTI) was used to derive in vivo tissue status measurements of subcortical brain regions that are vulnerable to injury in human immunodeficiency virus (HIV)-infected patients. Quantitative measurements, including the mean diffusivity (MD) and fractional anisotropy (FA), were determined in lateralized basal ganglia (caudate and putamen) and centrum semiovale in 11 well-characterized HIV patients and in 11 control subjects. DTI measurements were examined for patterns of relationship with markers of clinical and cognitive progression. DTI measures acquired in subcortical regions were significantly correlated with loss of function in specific cognitive domains. Significant relationships were identified between measures for putamen and verbal memory (MD), visual memory (FA), working memory (FA), and overall cognitive impairment (MD). Measures for caudate (FA) were significantly correlated with visual memory. Measures for centrum semiovale were significantly correlated with visual memory deficits (MD) and visuoconstruction (FA). Relationships between anisotropy measures and anemia (basal ganglia) and CD4 counts (centrum semiovale) were also observed. Findings from this investigation indicate that DTI is a sensitive tool for correlating neuroanatomic pathologic features with specific cognitive deficits in patients with HIV infection.