ObjectiveTo test the hypothesis that systemic and inhaled glucocorticoid use is associated with changes in grey matter volume (GMV) and white matter microstructure.DesignCross-sectional study.SettingUK Biobank, a prospective population-based cohort study of adults recruited in the UK between 2006 and 2010.ParticipantsAfter exclusion based on neurological, psychiatric or endocrinological history, and use of psychotropic medication, 222 systemic glucocorticoid users, 557 inhaled glucocorticoid users and 24 106 controls with available T1 and diffusion MRI data were included.Main outcome measuresPrimary outcomes were differences in 22 volumetric and 14 diffusion imaging parameters between glucocorticoid users and controls, determined using linear regression analyses adjusted for potential confounders. Secondary outcomes included cognitive functioning (six tests) and emotional symptoms (four questions).ResultsBoth systemic and inhaled glucocorticoid use were associated with reduced white matter integrity (lower fractional anisotropy (FA) and higher mean diffusivity (MD)) compared with controls, with larger effect sizes in systemic users (FA: adjusted mean difference (AMD)=−3.7e-3, 95% CI=−6.4e-3 to 1.0e-3; MD: AMD=7.2e-6, 95% CI=3.2e-6 to 1.1e-5) than inhaled users (FA: AMD=−2.3e-3, 95% CI=−4.0e-3 to −5.7e-4; MD: AMD=2.7e-6, 95% CI=1.7e-7 to 5.2e-6). Systemic use was also associated with larger caudate GMV (AMD=178.7 mm³, 95% CI=82.2 to 275.0), while inhaled users had smaller amygdala GMV (AMD=−23.9 mm³, 95% CI=−41.5 to −6.2) than controls. As for secondary outcomes, systemic users performed worse on the symbol digit substitution task (AMD=−0.17 SD, 95% CI=−0.34 to −0.01), and reported more depressive symptoms (OR=1.76, 95% CI=1.25 to 2.43), disinterest (OR=1.84, 95% CI=1.29 to 2.56), tenseness/restlessness (OR=1.78, 95% CI=1.29 to 2.41), and tiredness/lethargy (OR=1.90, 95% CI=1.45 to 2.50) compared with controls. Inhaled users only reported more tiredness/lethargy (OR=1.35, 95% CI=1.14 to 1.60).ConclusionsBoth systemic and inhaled glucocorticoid use are associated with decreased white matter integrity and limited changes in GMV. This association may contribute to the neuropsychiatric side effects of glucocorticoid medication, especially with chronic use.