Neural circuits in the central nervous system are the substrate of various high-order brain functions. However, little is known about the mechanisms underlying neuronal information processing in the brain. Anatomical and functional graph structures of neural networks with actual connections will provide us with perspectives to elucidate the brain complexity. Here, we aim to develop a three-dimensional mouse brain atlas of neural circuits using nano-resolution x-ray tomography by synchrotron radiation. In addition to identifying a large number of synapses, our research will also clarify the structure of neuronal networks for understanding the most complex organ in the body. In this study, we observed metal-stained biological tissues of the mouse brain using hard x-ray Zernike-type phase-contrast microscopy with 60-nm resolution at SPring-8. As a result, the nano-resolution hard x-ray phase-contrast microscope revealed nerve fibers and organelles including mitochondria and synapses in the neural tissue. In the near future, this information will be utilized to begin deciphering the wiring diagram of the brain by using nano-resolution x-ray tomography.