The magnetic resonance (MR) imaging patterns of HIV-infected patients affected by progressive multifocal leukoencephalopathy (PML) in the HAART era have not been extensively documented. The aim of the present study is to describe the MR features of PML in HIV-infected patients at diagnosis, and the evolution during follow-up, evaluating the impact of HAART on imaging, and to correlate the MR pattern with the virological and immunological levels and with survival. We retrospectively reviewed MR imaging at baseline and at the last available follow-up within 6 months of diagnosis (median 4 months, range 1-6) of 31 HIV-positive patients affected by PML. A closer follow-up [median interval from diagnosis 39 days (range 20-139)] was also reported. At the onset of neurological disorder, 19 patients were naive for antiretroviral therapy, 7 patients were on HAART, and 5 patients were experienced but were not taking antiretroviral therapy. Upon PML diagnosis no significant differences at imaging were observed between naive and experienced patients and HAART-treated or non-HAART-treated patients. MR findings were not related to immunological status, either at baseline or at follow-up. A radiological improvement within 6 months was associated with a higher probability of a more favorable clinical evolution [OR 14.0 (2.2-87.2), p = 0.003]. The overall probability of survival at 6 months was 61.5%. A better survival was observed in patients with stable or improved MR imaging findings within 6 months [HR 4.55 (95%CI 1.36-15.19, p = 0.009]. Although HAART prolonged the survival of HIV-positive patients affected by PML, it did not seem to influence the PML MR pattern of presentation and the imaging evolution. Only the radiological outcome was predictive of clinical outcome.