Cytomegalovirus (CMV) disease is associated with a high mortality in recipients of an allogeneic stem cell transplant. Apparent differences in biological behaviour have been noted among clinical CMV isolates. By amplifying specific functionally relevant regions of the CMV genome [immediate early (IE) exon 3, glycoprotein B (gB)], a possible association of strain variation and clinical symptoms of infection was analysed in 24 patients. A high number of genome mutations of the IE exon 3 region could be documented translating into amino acid changes of viral isolated of 8 out of 15 patients with symptomatic and 2 out of 9 patients with asymptomatic CMV infection. Identical IE mutations and gB types were observed in isolates from two different sites in 6 patients. gB strain 2 was found to be associated with symptomatic CMV infection (P = 0.03). Thus, apart from host factors viral factors might influence the virus-host interaction in severely immunosuppressed patients.