Human herpesviruses have been recognized as a pathogen involved in interstitial pneumonia (IP), especially in immunocompromised patients. So far, little is known about involvement of human herpesvirus 6 (HHV-6) in systemic respiratory tract disease. Currently, routine diagnostic tests for HHV-6 are inefficient for HHV-6 reactivation, therefore, we established a rapid quantification system of HHV-6 using real-time PCR in order to determine the possible role of human HHV-6 reactivation in immunocompromised patients showing IP. Bronchoalveolar lavage fluid (BALF) specimens were obtained from 84 consecutively treated patients with interstitial lung diseases (ILD) including various types of IP. First, we determined the viral burden in BALF and peripheral blood obtained from healthy volunteers. In healthy volunteers, the prevalence of HHV-6 in BALF was higher (4/12, 33.3%) than in peripheral blood (8/53, 15.1%), ranging from 0 to 101.65 HHV-6 genome copies per 1 microg of DNA. Among 84 patients with ILD analyzed, the prevalence of HHV-6 in BALF was 27.4% (23/84), ranging from 0 to 103.87 copies per 1 microg of DNA. Three specimens obtained from patients with collagen vascular disease, 2 from Hodgkin's disease, and 1 with sarcoidosis had high level of HHV-6 viral DNA, while none of the patients with idiopathic IP showed elevation of HHV-6 (more than 102) in BALF. Our results suggest that measurement of HHV-6 genomes in BALF using real-time PCR may be useful in management of the care of respiratory complications in immunocompromised patients.