Real-time polymerase chain reaction (PCR) and pp65 antigenemia assay for the detection of active cytomegalovirus infection in immunocompromised patients experiencing neutropenia after bone marrow or kidney transplantation have been compared with a special focus on evaluability and embedment in daily routine diagnostics. Investigating 334 specimens from 97 patients, real-time PCR was shown to be the superior assay with regard to the parameters focused on.