Magnetic resonance fingerprinting (MRF) permits simultaneous acquisition of T1 and T2 maps perfectly aligned to the anatomy, allowing morphometry and relaxometry analysis of the brain in a single scan. Here, we examined the reproducibility and repeatability of simultaneous morphology and relaxometry of brain structures in healthy volunteers using three-dimensional MRF at multiple field strengths. Scan-rescan tests of three-dimensional MRF were performed at 1.5 and 3T. The local thickness, volume, T1, and T2 values were calculated for each representative neuroanatomical structure using automatic brain segmentation software. These results can help establish imaging biomarkers using MRF for clinical use.