We performed laboratory investigations of the image quality for in-line phase contrast micro tomography dedicated to the breast, using a 3D breast phantom. We employed the cone-beam, microfocus (7-micrometer focal spot size) computed tomography (CT) scanner developed in-house for investigation of high resolution, absorption based, and phase contrast based, X-ray imaging of the breast for cancer diagnosis, at dose levels comparable to two-view mammography. CT slices were reconstructed (FDK algorithm) from phase contrast projection images as well as from phase retrieved projections (ANKAphase algorithm), under the assumption of spatially uniform distribution in the object volume of the ratio of the X-ray optical coefficients of the sample material, at the effective energy of the X-ray beam (80 kV, HVL = 6.11 mm Al). Microcalcifications were best visible after phase retrieval, down to 0.23 mm size.