Multi-shell diffusion MRI sampling schemes require long acquisition times and are hence potentially compromised by poorer subject compliance. There is therefore a need to consider strategies to enable shortening the exam to ensure clinical feasibility, while maintaining cross-exam comparability. We analyzed the impact of subsampling a multi-shell scheme on the estimation of diffusion maps. In particular, we evaluated its effect on histogram-derived metrics computed over skeletonized maps of DTI and DKI parameters. Several metrics showed a significant effect of subsampling. This should be carefully considered depending on the effect size we are trying to measure on a patient’s population.