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Long-term survival after lung transplantation remains limited by the development of bronchiolitis obliterans syndrome (BOS). Allograft colonization with Pseudomonas aeruginosa is common particularly in recipients with BOS, but a possible etiological relationship remains unexplored. In 155 consecutive lung transplants, the development of allograft colonization with Pseudomonas was strongly associated with the development of BOS within 2 years of transplant (23.4% vs. 7.7% in those colonized and not colonized, respectively, P=0.006). Freedom from BOS was significantly shorter in those patients without any pretransplant bacterial reservoir developing de novo allograft pseudomonal colonization as compared with those remaining free of colonization (Kaplan-Meier log-rank P=0.014). The isolation of Pseudomonas preceded the diagnosis of BOS in 14 of 18 (78%) and by a median of 204 days (95% confidence interval 115–492) in patients developing both these complications. We conclude that de novo colonization of the lung allograft by Pseudomonas is strongly associated with the subsequent development of BOS.