An electron density map projected along the direction of the incident X-ray is obtained from a single small-angle diffraction pattern. However, most projection maps are difficult to interpret. The final goal of a structural analysis is a visualization of the electron density distribution in three dimensions. In this chapter, the tomography X-ray diffraction imaging (XDI) method is first introduced to visualize three-dimensional (3D) electron density maps of particles in XDI using synchrotron radiation. In XDI experiments using X-ray free electron laser (XFEL) pulses, as the specimen particles are destroyed by single X-ray pulses, tomography experiments are impossible. Under the assumption that the structures of the particles are similar at a low resolution, 3D reconstruction is possible by utilizing the single particle analysis method developed in transmission electron microscopy (TEM). A scheme for 3D reconstruction in XFEL-XDI through simulations for macromolecules and experiments on a cellular organelle is proposed.