Few studies have examined the prevalence and cellular proclivity of latent human herpesyirus 6 (HHV-6) in healthy populations. Difficulties in detection of HHV-6 genome in different tissues using polymerase chain reaction (PCR) and immunohistochemistry (IHC) techniques have been reported by various researchers. We examined tonsils and adenoid tissues of 54 patients who had undergone tonsillectomy or adenoidectomy without any evidence of acute infection for the presence of latent HHV-6 infection. While we were investigating the prevalence of HHV-6, we tested the efficiency of PCR, IHC and Western Blot (WB) for detection of HHV-6 in tonsil tissues. We found that 100% of tonsil tissues were positive for HHV-6 with WB, 40% of tonsils were positive with PCR and no tonsil was positive with IHC. This result correlates well with most studies claiming HHV-6 is a ubiquitous organism in various populations and tissues. Western blot may be a good choice for detecting HHV-6 in tissues. Expression of the HHV-6 gp60/110 envelope protein disclosed by WE may indicate that HHV-6 does not have true latency. To our knowledge, this is the first report to use WB to test for HHV-6 in tissues.