Variations in modern head-coil design lead to sensitivity differences, changes in intensity profiles, and image SNR. As morphometric analysis is based on automated analysis of image intensity and contrast variations, such variation of head coil may be expected to provide variation in morphometric results. We investigated the morphometric results from MEMPRAGE scans on subjects scanned in pairs of different head coils. We saw very limited variation in basic morphometric results from subjects scanned on the same day in different head coils. Cortical thickness variations are generally less than 50 µm, although some larger values were observed in portions of the temporal lobe. Larger differences were observed in volumes of small sub-cortical structures. These structures often have high variability in repeat measurements. However, intensity and SNR variations between coils are often most felt in the deeper regions of the brain, perhaps contributing to wider variation for these structures.