Bronchiolitis obliterans syndrome (BOS) is a major cause of late graft dysfunction in lung transplant recipients. There is increasing evidence that beside alloimmunologic injury also non-alloimmunologic inflammatory conditions may raise the risk of acute and chronic rejection. The oral cavity represents a possible reservoir for pathogenic bacteria due to its close anatomical proximity. In this pilot study, the presence of pathogenic periodontal bacteria in the oral cavity as well as in the lungs of lung transplant recipients was investigated for the first time. Eight lung transplant recipients underwent broncho-alveolar lavage, transbronchial biopsies, and endobronchial biopsies. In addition to routinely performed examinations, pulmonary as well as plaque samples were assessed for Aggregatibacter actinomycetemcomitans (Aa), Tannerella forsythia (Tf), Porphyromonas gingivalis (Pg), and Treponema denticola (Td) with the aid of a hybridization technique. No or only one periodontal pathogen (solitarily Pg) was found in the gingival plaques of five of the eight patients (group A). In three patients, two or more periodontal pathogens were detetectable in the gingival samples (group B). Whereas group A also had not more than one periodontal pathogen in the lungs, group B had more than one species in the lungs. In group B, all patients suffered from BOS, whereas in group A only one patient was affected. This is the first evidence for the presence of periodontal pathogens in the lungs of lung transplant recipients. Further studies with larger cohorts are required to elucidate potential links between periodontal infection, pulmonary colonization, and rejection.