We have imaged the three-dimensional density distribution of unstained and unsliced, freeze-dried cells of the gram-positive bacterium Deinococcus radiodurans by tomographic x-ray propagation microscopy, i.e. projection tomography with phase contrast formation by free space propagation. The work extends previous x-ray imaging of biological cells in the simple in-line holography geometry to full three-dimensional reconstruction, based on a fast iterative phase reconstruction algorithm which circumvents the usual twin-image problem. The sample is illuminated by the highly curved wave fronts emitted from a virtual quasi-point source with 10 nm cross section, realized by two crossed x-ray waveguides. The experimental scheme allows for a particularly dose efficient determination of the 3D density distribution in the cellular structure.