The neuroanatomical architecture is considered to be the basis for understanding brain function and dysfunction. However, existing imaging tools have limitations for brainwide mapping of neural circuits at a mesoscale level. We developed a micro-optical sectioning tomography (MOST) system that can provide micrometer-scale tomography of a centimeter-sized whole mouse brain. Using MOST, we obtained a three-dimensional structural data set of a Golgi-stained whole mouse brain at the neurite level. The morphology and spatial locations of neurons and traces of neurites could be clearly distinguished. We found that neighboring Purkinje cells stick to each other.