BACKGROUND: Lung transplantation provides a unique opportunity to investigate the dynamics of the human pulmonary virome that is transplanted within the donor lungs. The pulmonary virome comprises both "resident" and "transient" viruses. In this study we aimed to analyze the dynamics of the "transient" members. METHODS: We conducted a single-center, prospective, longitudinal investigation of community-acquired respiratory viruses detected in nasopharyngeal swabs, swabs of explanted and donor lungs, and serial bronchoalveolar lavages post-transplant. RESULTS: Fifty-two consecutive lung transplant recipients were recruited (bilateral:heartlung:bilateral lung-liver=48:2:2) (age [mean +/- SD] 48 +/- 15 years, range 20 to 63 years; 27 males and 25 females). Follow-up was 344 +/- 120 (range 186 to 534) days. Seventeen of 45 explanted lungs were positive for influenza A and/or B (A=14, B=2, A+B=1), despite recipient vaccination and negative nasal swabs, and 4 of 45 had human rhinovirus and 2 of 45 parainfluenza. Donor swabs showed influenza (A=1, B=1) and rhinovirus (n=3). Day 1 lavage showed influenza A (n=28), rhinovirus (n=9), and parainfluenza (n=1). Forty-seven of 52 recipients had a positive lavage for virus (38 of 47 on multiple lavages). Influenza persisted for 59 +/- 38 (range 4 to 147) days in 27 of 52, and 14 had a single isolate. Rhinovirus persisted for 95 +/- 84 (range 22 to 174) days in 13 of 52, and 13 had a single isolate. Analysis of 118 paired transbronchial biopsies and lavage demonstrated no association between viruses and acute cellular rejection (Fisher\'s exact test, 2 tailed, p=1.00). CONCLUSIONS: Using a sensitive uniplex polymerase chain reaction we found that the transplanted pulmonary virome often includes community-acquired respiratory viruses, including influenza, which are variably persistent but not associated with acute rejection.