Respiratory viral pathogens are a common cause of morbidity in patients with hematologic malignancies. Sensitive molecular assays have increased the detection of common respiratory viruses and expanded the panel of detectable viruses. Both a rapid viral culture with direct fluorescence antibody (DFA) staining and a PCR-based assay (MultiCode-PLx Respiratory Virus Panel) were performed on patients with hematologic malignancies, who underwent collection of a nasopharyngeal swab or bronchoalveolar lavage from October 2006 to April 2007. Eighty-two samples from 70 patients were obtained; all patients had upper respiratory tract symptoms. Respiratory viruses were detected in 10 samples (12%) by conventional virological methods and in 31 samples (38%) by the MultiCode-PLx assay. This increased diagnostic yield resulted from better sensitivity for those viruses detectable by both methods and detection of viruses not covered by the antigen detection/rapid culture method (human metapneumovirus, coronaviruses and rhinoviruses). The MultiCode-PLx assay frequently identified respiratory viral infections which are not detected by rapid viral culture/DFA; 40% of these patients had pneumonia in addition to the upper respiratory tract symptoms. Improved diagnostics for respiratory viruses may lead to more effective management and better outcomes in this patient population.