Consider an i.i.d. sample from an unknown density function supported on an unknown manifold embedded in a high dimensional Euclidean space. We tackle the problem of learning a distance between points, able to capture both the geometry of the manifold and the underlying density. We define such a sample distance and prove the convergence, as the sample size goes to infinity, to a macroscopic one that we call Fermat distance as it minimizes a path functional, resembling Fermat principle in optics. The proof boils down to the study of geodesics in Euclidean first-passage percolation for nonhomogeneous Poisson point processes.