HIV-1 RNA and neopterin levels were observed longitudinally for 20 to 68 months (mean, 37.5 months) in cerebrospinal fluid (CSF) and serum in 15 HIV-1-infected patients not receiving antiretroviral treatment. During the course of infection the HIV-1 RNA levels increased significantly in CSF, from a mean of 3.08 to 3.51 log10 copies RNA/ml (p < .01). A significant positive correlation was found between the CSF levels of HIV-1 RNA and neopterin (rs = 0.54; p < .001), which increased from 13.6 to 19.6 nmol/L (p < .01). No significant changes in HIV-1 RNA or neopterin levels were found in serum. We suggest that the increase of CSF viral load with time in HIV-1 infection triggers an intrathecal immune activation reflected by increased CSF levels of neopterin. These results are in accordance with the theory that a chronic immune stimulation within the central nervous system (CNS) is involved in the pathogenesis of neurologic HIV-1 disease.