The use of highly active anti-retroviral therapy in patients with HIV-related progressive multifocal leukoencephalopathy is associated with increased survival and disease stabilization. However, approximately half of the patients receive no benefit from these treatments. In a group of HIV-infected patients with histologically or virologically confirmed PML, we recognized two distinct patterns of response, i.e., long survivors versus nonresponders, but could not identify any factors at baseline predictive of PML outcome. In addition, the use of cidofovir did not substantially affect survival. However, the survival rate was higher during the first years of HAART, i.e., 1996-1997, with better outcomes observed in patients receiving a protease inhibitor-containing regimen either irregularly or after a switch from a 2-nucleoside reverse transcriptase inhibitor combination. In contrast, PML outcome was frequently poor in both HAART-naive and -experienced patients who responded promptly to anti-HIV therapy in terms of CD4 increase and viral load decrease. In addition, in a number of patients, PML onset was temporally associated with immune reconstitution. It may be that, in some patients, rapid immune reconstitution due to HAART paradoxically worsens the course of PML. Gradual reversal of immune deficiency might be associated with better outcome.