Progressive multifocal leukoencephalopathy (PML) is a fetal demyelinating disease in the central nervous system. PML was once a rare disease, but it is now relatively common among AIDS (acquired immunodeficiency syndrome) patients. The immunological state of patients mainly contributes to the pathogenesis of PML. Genetic changes of the etiological agent, however, may also be involved in the development and progression of the disease. The major genetic changes possibly associated with PML include the regulatory region rearrangement and the VP1 loop mutation. Both changes have been identified as genetic changes usually occurring in JCV (JCvirus) DNAs from the brain and cerebrospinal fluid of PML patients. Although it remained to be clarified how these changes are involved in the pathogenesis of PML, accumulating evidence suggests that the VP1 loop mutation is associated with the progression of PML. Here we overview studies (mainly those performed by ourselves) on these genetic changes.