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Background Nocturnal gastro-oesophageal reflux (nGER) is common in people with respiratory diseases, but its association with pulmonary abnormalities is not known.Aim Investigate the association between nGER and pulmonary abnormalities on chest CT in an adult general population.Methods In total, 28 846 individuals from the general population aged 50–64 years completed questionnaires and underwent chest CT, in the Swedish CArdioPulmonary BioImage Study ( www.scapis.org). Participants with nGER symptoms on ≥1 night per week were defined as having nGER. Chest CT was evaluated for bronchial wall thickening, bronchiectasis, reticular abnormalities, honeycombing, cysts and ground glass opacities. Ever-smoking, current asthma, inflammatory bowel disease and autoimmune disease were defined as risk factors for pulmonary abnormalities. Analyses were adjusted for sex, age, body mass index, education level and study centre.Results The prevalence of nGER was 9.4%. Among participants with risk factors for pulmonary abnormalities (n=4004), having nGER was positively associated with bronchial wall thickening (adjusted OR (aOR) (95% CI): 1.25 (1.07 to 1.48)) and reticular abnormalities (aOR (95% CI): 1.51 (1.04 to 2.17)), but negatively associated with cysts (aOR (95% CI): 0.68 (0.48 to 0.97)). Among participants without risk factors for CT abnormalities (n=2555), nGER did not relate with pulmonary abnormalities.Conclusions In a middle-aged general population, nGER was not associated with pulmonary abnormalities on chest CT. However, in the presence of other risk factors for pulmonary abnormalities, nGER was associated with bronchial wall thickening and reticular abnormalities. Persons with nGER and risk factors for pulmonary abnormalities should, therefore, be evaluated for respiratory disease and treated appropriately.