©2017 Samuel Gerber and Mauro Maggioni. This paper presents a multiscale approach to efficiently compute approximate optimal transport plans between point sets. It is particularly well-suited for point sets that are in high-dimensions, but are close to being intrinsically low-dimensional. The approach is based on an adaptive multiscale decomposition of the point sets. The multiscale decomposition yields a sequence of optimal transport problems, that are solved in a top-to-bottom fashion from the coarsest to the finest scale. We provide numerical evidence that this multiscale approach scales approximately linearly, in time and memory, in the number of nodes, instead of quadratically or worse for a direct solution. Empirically, the multiscale approach results in less than one percent relative error in the objective function. Furthermore, the multiscale plans constructed are of interest by themselves as they may be used to introduce novel features and notions of distances between point sets. An analysis of sets of brain MRI based on optimal transport distances illustrates the effectiveness of the proposed method on a real world data set. The application demonstrates that multiscale optimal transport distances have the potential to improve on state-of-the-art metrics currently used in computational anatomy.