Inflammatory injuries directed toward airway structures play a key role in lung allograft rejection. However, data relating to the inflammation patterns of large airways are scarce and, in particular, the relation between autologous and allogeneic parts is unknown. For the first time, in this study, simultaneously collected endobronchial biopsies from the main (autologous) and upper lobe (allogeneic) carina of lung transplant recipients were assessed immunohistologically. A total of 27 pairs of EBBs were taken. Twelve endoscopies documented acute rejection and four examinations of patients with BOS were performed. Patients with acute rejection had more CD8-positive cells in the allogeneic parts compared with patients without acute rejection. Patients with BOS had more CD4- and CD45-positive cells in the autologous airways than stable patients. We conclude that distinct inflammatory changes do occur in large airways of lung transplant recipients and are not limited to the donor parts of airways.