The objective of this study was to characterize the sensitivity of voxel-based morphometry (VBM) results to choice field strength. We chose to investigate the two most widespread acquisition sequences for VBM, FLASH and MP-RAGE, at 1.5 and 3 T. We first evaluated image quality of the four acquisition protocols in terms of SNR and image uniformity. We then performed a VBM study on eight subjects scanned twice using the four protocols to evaluate differences in grey matter (GM) density and corresponding scan-rescan variability, and a power analysis for each protocol in the context a longitudinal and cross-sectional VBM study. As expected, the SNR increased significantly at 3 T for both FLASH and MP-RAGE. Image non-uniformity increased as well, in particular for MP-RAGE. The differences in CNR and contrast non-uniformity cause regional biases between protocols in the VBM results, in particular between sequences at 3 T. The power analysis results show an overall decrease in the number of subjects required in a longitudinal study to detect a difference in GM density at 3 T for MP-RAGE, but an increase for FLASH. The number of subjects required in a cross-sectional VBM study is higher at 3 T for both sequences. Our results show that each protocol has a distinct regional sensitivity pattern to morphometric change, which goes against the classical view of VBM as an unbiased whole brain analysis technique, complicates the combination of data within a VBM study and the direct comparison of VBM studies based on different protocols. Hum Brain Mapp, 2010. © 2009 Wiley-Liss, Inc.