PURPOSE OF REVIEW: Chronic allograft failure remains the leading cause of late mortality following lung transplantation. Considerable evidence demonstrates a relationship between gastroesophageal reflux disease (GERD) induced allograft injury and bronchiolitis obliterans syndrome; however, the mechanism of injury, identification of at-risk patients, and treatment options remain to be elucidated. RECENT FINDINGS: The recent findings in this area help delineate the inflammatory pathways associated with GERD-induced lung injury. They also demonstrate that clinically useful markers of aspiration-induced injury may be available via studying bronchoalveolar fluid or even induced sputum. Simple acid neutralization is not adequate to protect these patients from aspiration injury. In fact, there are no convincing data to indicate that medical therapies provide adequate treatment. In contradistinction, surgical fundoplication is associated with decreased levels of inflammatory cytokines and markers of aspiration in bronchoalveolar fluid, as well as improvements in pulmonary function in these patients. SUMMARY: Recent findings support ubiquitous testing for GERD or aspiration in patients with end-stage lung disease both pretransplant and posttransplant and demonstrate that fundoplication can safely and effectively protect these patients from the on-going injury of GERD-induced pulmonary injury.