To assess the relationship of longitudinal brain magnetic resonance imaging (MRI) and infection with human immunodeficiency virus (HIV), a cohort of HIV+ and HIV− gay men and injection drug users (IDU) were evaluated prospectively. Subjects underwent two evaluations including MRI scans, neurologic examinations, neuropsychological assessments and lymphocyte subset determinations one year apart. MRI changes over a one year period were analyzed with respect to serostatus, risk group, CD4 counts, neurological findings and neuropsychological performance. The frequency of MRI changes was no different in subjects with or without HIV infection and no new opportunistic infections or neoplasms were seen. However, among HIV+ subjects with CD4 count < 200 at the time of the initial scan, an increase in white matter hyperintensities was significantly more common. Also among HIV+ subjects, atrophy increased in association with declining CD4 count. Finally, subjects who developed significant neurologic deterioration in one year were much more likely to have increased atrophy. These results suggest that while there are morphological brain changes associated with HIV infection, they are most often seen in association with immunologic or neurologic deterioration.