The morbidity and mortality rates of cytomegalovirus (CMV) infections, including pneumonitis in bone marrow transplant patients, are well documented and yet no rapid, sensitive diagnostic tool is available. To test the polymerase chain reaction as such a diagnostic tool, formalin-fixed, paraffin-embedded open lung biopsy material was selected from post-bone marrow transplant patients in whom pulmonary parenchymal changes were evident but viral inclusions were not seen. As a control, other immunosuppressed (non-bone marrow transplant) patients and low-risk nonimmunosuppressed patients were studied in a similar manner. Viral culture results and clinical data were available on all the high-risk patients. Two of 15 high-risk patients were found to have amplifiable CMV DNA despite the lack of histologic viral inclusions. One of these patients had been treated recently for CMV pneumonia, and the other had a positive culture of the lung specimens for CMV 13 days after biopsy. None of 12 control patients had amplifiable CMV DNA. These data indicate that the polymerase chain reaction is more sensitive than histologic examination and at least as sensitive as viral culture without evidence of false-positive results.