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Objectives: To investigate whether clinical condition, imaging session, and locations affect repeatability of amide proton transfer-weighted (APTw) magnetic resonance imaging (MRI) in the brain., Materials and Methods: Three APTw MRI data sets were acquired, involving two intrasession scans and one intersession scan for 19 healthy, 15 glioma, and 12 acute stroke adult participants (mean age 53.8, 54.6, and 68.5, respectively) on a 3T MR scanner. The mean APTw signals from five locations in healthy brain (supratentorial and infratentorial locations) and from entire tumor and stroke lesions (supratentorial location) were calculated. The within-subject coefficient of variation (wCV) and intraclass correlation coefficient (ICC) were calculated for each clinical conditions, image sessions, and anatomic locations. Differences in APTw signals between sessions were analyzed using repeated-measures analysis of variance., Results: The ICC and wCV were 0.96 (95% confidence interval [CI], 0.91-0.99) and 16.1 (12.6-21.3) in glioma, 0.93 (0.82-0.98) and 15.0 (11.4-20.6) in stroke, and 0.84 (0.72-0.91) and 34.0 (28.7-41.0) in healthy brain. There were no significant differences in APTw signal between three sessions, irrespective of disease condition and location. The ICC and wCV were 0.85 (0.68-0.94) and 27.4 (21.8-35.6) in supratentorial, and 0.44 (- 0.18 to 0.76) and 32.7 (25.9 to 42.9) in infratentorial locations. There were significant differences in APTw signal between supra- (mean, 0.49%; 95% CI, 0.38-0.61) and infratentorial locations (1.09%, 0.98-1.20; p < 0.001)., Conclusion: The repeatability of APTw signal was excellent in supratentorial locations, while it was poor in infratentorial locations due to severe B0 inhomogeneity and susceptibility which affects MTR asymmetry., Key Points: • In supratentorial locations, APTw MRI showed excellent intrasession and intersession repeatability in brains of healthy controls and patients with glioma, as well as in stroke-affected regions. • APTw MRI showed excellent repeatability in supratentorial locations, but poor repeatability in infratentorial locations. • Considering poor repeatability in the infratentorial locations, the use of APTw MRI in longitudinal assessment in infratentorial locations is not indicated.