Efforts to reduce relapse of non-Hodgkin lymphoma after autologous transplantation have included ex vivo stem cell selection and/or peritransplantation immunotherapy. The late infectious and immunologic consequences of these maneuvers are not well understood, although an increase in early cytomegaloviral disease after CD34(+) stem cell selection and an alteration in immunoglobulin and T-cell recovery after peritransplantation rituximab has been noted. We report the first 2 cases of progressive multifocal leukoencephalopathy caused by JC papovavirus after autologous peripheral blood stem cell transplantation and a case each of cytomegalovirus retinitis and pneumonitis. All 4 patients experienced significant impairment of CD4 T-cell recovery, placing them at risk for these unusual viral infections. The clustering of cases is concerning because all occurred shortly after the introduction of peritransplantation rituximab into treatment protocols (4 of 62 immunotherapy recipients compared with 0 of 276 without; z = 3.595; P <.001), although a direct association with this CD20 B-cell-directed therapy remains speculative.