Bayesian model fitting has been shown to yield robust estimates of the IVIM parameters. However, various methodological choices have differed between studies, which may have substantial effect on the results. This study investigates the effect that the prior distributions and central tendency measures may have, using both in vivo data and simulations. The results show that the prior distribution can play a significant role at commonly seen signal-to-noise levels. The choice of central tendency measure has less effect on the estimates. However, it may be chosen to emphasize either accuracy or precision.