This thesis presents two novel three-dimensional (3D) phase-retrieval methods for propagation-based X-ray phase-contrast tomography (PB-CT). The first method uses the homogeneous form of the transport-of-intensity equation (TIE-Hom). The second method employs the contrast-transfer-function (CTF) formalism, which is further extended to the cases of partially-coherent illumination and strongly absorbing samples. Unlike conventional PB-CT that performs phase retrieval on individual projections, these post-reconstruction phase-retrieval methods are applied in 3D. Simulated results demonstrate that the proposed methods are fast and stable, producing results equivalent to conventional pre-reconstruction TIE and CTF phase retrieval. Moreover, the post-reconstruction methods can be highly localised to isolated objects of interest, without a significant loss of quality, thus leading to increased computational efficiency.