Structural and functional brain abnormalities have been reported in chronic obstructive pulmonary disease (COPD), however, it is unclear whether these occur independently of cardiovascular risk. Neuroimaging and clinical markers of brain structure and function were compared between 27 COPD patients and 23 age-matched non-COPD smoker controls. Clinical relationships and group interactions with brain structure were tested. COPD patients showed a specific pattern of structural (lower grey matter volume) and functional (lower cognitive function and psychological status) brain abnormalities that could not be explained by cardiovascular risk. Lower lung function and psychological ill-health were associated with markers of white matter damage.