Background It is common experience that retreating patients too early after a course of intensive chemotherapy predisposes to opportunistic infections despite apparently normal lymphocyte levels. Objectives The extent of replication of persistent viruses that cause no obvious disease (and hence need no treatment) might better define when a patient has recovered from functional immune deficiency. Study design We used real-time polymerase chain reaction to monitor the kinetics of plasma torquetenovirus (TTV) viremia in hematological patients undergoing autologous hematopoietic stem cell transplantation as support to high-dose chemotherapy (HSCT). Results Independently from underlying hematological disease and therapeutic regimen, TTV viremia increased post-HSCT, and this increase paralleled the increase of circulating CD8 +CD57 + T lymphocytes, known to represent an indirect marker of functional immune deficiency. Subsequently, within a matter of months, TTV levels returned to baseline values, at a pace that appeared to be constant over time. Conclusion Monitoring of TTV viremia represents a unique opportunity to follow functional immune reconstitution in immunosuppressed patients. Also, the size of the TTV viremia increases resulting from immunosuppressive treatments might be of guidance in determining the appropriate time interval before delivery of a next course of therapy.