7 Tesla (7T) magnetic resonance imaging (MRI) holds great promise for improved visualization of the human brain for clinical purposes. To assess whether 7T MRI is superior regarding localization procedures of small brain structures, we compared manual parcellations of the red nucleus (RN), subthalamic nucleus (STN), substantia nigra (SN), globus pallidus interna and externa (GPi and GPe) created on a commonly used clinical anisotropic (c)3T with an optimized isotropic (o)3T and standard 7T MRI scan. While the c3T MRI scan did not allow for a quantitative assessment due to its limited spatial resolution, o3T and 7T parcellations could be directly compared. We found that 7T outperformed the o3T MRI as reflected by higher Dice scores, which were used as a measurement of interrater agreement for manual parcellations on quantitative susceptibility maps (QSM). This increase in agreement was associated with higher contrast to noise ratios (CNRs) for the smaller RN, STN, and SN, but not for the larger GPi and GPe. Additionally, control-analyses were performed to account for potential biases in manual parcellations by assessing semi-automatic parcellations. These results did not confirm increased Dice scores for 7T, although they revealed a higher consistency for structure volumes for 7T compared to o3T, potentially indicative of more agreement with increased field strength. Together these results indicate the importance of the use of isotropic voxels and the potential of 7T MRI for clinical applications.