In previous prospective studies conducted in our department, PCR was used to detect the three β-herpesviruses, human cytomegalovirus (HCMV), and human herpesviruses 6 and 7 (HHV-6 and HHV-7) in the blood of solid organ transplant patients. The viruses were commonly detected post-transplantation, and HCMV and HHV-6 were independently associated with graft rejection in liver recipients. HHV-7 was also associated with increased episodes of rejection in renal transplant patients. To better understand the role of these viruses in graft rejection, in situ techniques including in situ hybridisation (ISH) and immunohistochemistry (IHC) were developed to detect these viruses in renal and liver allograft biopsies from patients in the original prospective studies. HCMV DNA was detected in a significant proportion of liver and renal biopsies (approximately 50%) by ISH, with detection being widespread especially in renal allografts. The presence of HCMV DNA in the biopsies is likely to represent low level HCMV replication not detectable by IHC. HCMV was not statistically associated with either renal or liver allograft rejection by ISH. It remains possible that HCMV infection in the graft leads to dysfunction and is clinically interpreted as allograft rejection. HHV-6 and HHV-7 were not detected in any allografts by ISH or IHC. In addition, an uncommon form of HHV-6 persistence is characterized by high viral loads in blood and integration of viral sequences into host cell chromosomes. Fluorescence in situ hybridisation (FISH) was developed to examine integration events in a healthy individual with a consistently high HHV-6 load and also in a case of genetic transmission of integrated virus through stem cell transplantation. In the former individual, integrated HHV-6 was identified on chromosome lip 15.5 and in the latter shown in the donor and the recipient (post-transplantation only) on chromosome 17pl3.3. The confounding effect of HHV-6 integration must be considered when investigating novel disease associations of HHV-6.