The development of ocular vessels is a complex, finely orchestrated sequence of events, involving spatial and temporal coordination of hyaloid, choroidal and retinal networks. Comprehensive studies of such processes are limited by the fact that preserving the entire three-dimensional morphology of ocular vascular networks is cumbersome using classical histological procedures. Here, we demonstrate that light-sheet fluorescence microscopy (LFSM) of cleared mouse eyes followed by extensive virtual dissection offer a solution to this problem. We show the first 3D quantification of the evolution of the hyaloid vasculature and of post-occlusive venous remodelling together with the characterization of spatial distribution of various cell populations in ocular compartments, including the vitreous. These techniques will prove interesting to obtain new insight in scientific questions where both organ-wide tissue interactions and cellular specificities need to be investigated simultaneously.