BACKGROUND: Scan acceleration such as parallel imaging reduces scan time, but shorter scan time may reduce the signal-to-noise ratio and affect image quality. The reproducibility of longitudinal changes in the brain structure between non-accelerated and accelerated imaging by surface-based analysis is unclear. PURPOSE: To determine the reproducibility of longitudinal changes in cortical thickness, measured by surface-based morphometry, between non-accelerated and accelerated structural T1 -weighted imaging in the healthy elderly and those with mild cognitive impairment (MCI) and Alzheimer's disease (AD). STUDY TYPE: Retrospective. SUBJECTS: Fifty healthy elderly subjects (age = 73 ± 5 years, 29 females, 21 males), 54 MCI patients (age = 71 ± 7 years, 23 females, 31 males), and 8 AD patients (age = 78 ± 6 years, 6 females, 2 males). FIELD STRENGTH/SEQUENCE: 3 T, magnetization-prepared rapid gradient-echo. ASSESSMENT: Longitudinal changes in cortical thickness estimated by the longitudinal stream in FreeSurfer from 2-year interval data, and visual assessment of image quality by three radiologists. STATISTICAL TESTS: Intraclass correlation coefficient (ICC) and Kruskal-Wallis test. A P value <0.05 was considered significant. RESULTS: Healthy elderly subjects, MCI patients, and AD patients showed different patterns in the ICC maps. For the smoothing of 20 mm full width at half maximum, the mean ICC was 0.45 overall (healthy elderly, 0.33; MCI patients, 0.49; AD patients, 0.31). The within-subject SDs of the symmetrized percent changes were similar between healthy elderly subjects (mean, 1.3%/year) and MCI patients (mean, 1.3%/year) but larger in AD patients (mean, 1.7%/year). Image quality did not significantly differ per group (P = 0.18). DATA CONCLUSION: The results of this study indicate the reproducibility of longitudinal changes in cortical thickness measured by surface-based morphometry between non-accelerated and accelerated imaging, and that the reproducibility varies by disease and region. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 1.