Our goal is to determine whether diffusion MRI acquisitions with different phase-encoding directions (PEDs) result in comparable quantitative measures in different regions of the human brain, or whether PEDs introduce a bias. Additionally, we aim to determine if for a given region, a set of PEDs has better reproducibility. For several regions, PA phase-encoding direction resulted in values that were significantly different than the other three. LR/RL phase-encoding was more reproducible compared to AP/PA in most brain regions, with frontal white matter being the exception. The main source of these reproducibility variations was identified as ghosts overlapping with brain regions.