A critical shortage of donor organs raises a question of needs for alternative organ sources for regenerative medicine. Over the last decade, three-dimensional (3D) culture has become a new approach for organ regeneration. The 3D culture takes significant advantages of cells spatial relationships between multiple cellular types and surrounding matrices of dynamic cellular interactions, which plays a key role in structural self-formation of complex organ buds. Here we present major classic cases of 3D culture organ regeneration to show how it works, and then we try to find the way of future organ regeneration.