Two of the four betaherpesviruses, Cytomegalovirus (CMV) and human herpesvirus 6B (HHV-6B), play an important role in opportunistic infections in hematopoietic stem cell transplant (HSCT) recipients. These viruses are ubiquitous in humans and can latently infect mononuclear lymphocytes, complicating the diagnosis of the diseases they cause. Although the detection of viral DNA in a patient’s peripheral blood by real-time PCR is widely used for monitoring viral infection, it is insufficient for the diagnosis of virus-associated disease. Theoretically, end-organ disease should be confirmed by detecting either viral antigen or significant amounts of viral DNA in a tissue sample obtained from the involved organ; however, this is often difficult to perform in clinical practice. The frequency of CMV-associated diseases has decreased gradually as a result of the introduction of preemptive or prophylactic treatments; however, CMV and HHV-6B infections remain a major problem in HSCT recipients. Measurement of viral DNA load in peripheral blood or plasma using real-time PCR is commonly used for monitoring these infections. Additionally, recent data suggest that an assessment of host immune response, particularly cytotoxic T-cell response, may be a reliable tool for predicting these viral infections. The antiviral drugs ganciclovir and foscarnet are used as first-line treatments; however, it is well known that these drugs have side effects, such as bone marrow suppression and nephrotoxicity. Further research is required to develop less-toxic antiviral drugs.