We have investigated theoretically the mean absorbed dose to the mouse in our newly constructed, in-line holography, x-ray phase-contrast, in-vivo, micro-CT system with an ultrafast laser-based x-ray (ULX) source. We assumed that the effective mouse diameter was 30 mm and the x-ray detector required minimum 30 μGy per frame to produce high quality images. The following laser target-filter combinations were considered: Ag-Ag, Mo-Mo, Sn-Sn. In addition, we considered narrow-pass multilayer x-ray mirrors. The corresponding ULX spectra were obtained using a CZT solid-state spectrometer. The approach used for dose computation was similar to human dose estimation. The mouse was modeled as a tissue-equivalent cylinder located at the isocenter with diameter 30 mm and density 1g/cm 3. A layer of dermis (skin and fur) with 1 mm thickness was also modeled. Imparted energy per volume was estimated for 1 keV wide x-ray energy intervals in the 6-100 keV range. Monte Carlo simulations were performed using the SIERRA code previously validated using 30 mm diameter PMMA phantom. The results obtained indicate that: a) the mean absorbed dose for ULX is less than or equal to that from a W-anode micro-CT tube operating at 30-40 kVp with 0.5 or 1.0 mm Al; b) for filter thickness above 100 μm, Sn-Sn results in the highest dose, followed by Ag-Ag and Mo-Mo; c) the multilayer x-ray mirror with FWHM ≤ 10 keV produces significantly lower dose than metallic foil filters. We conclude that ULX can provide better dose utilization than a microfocal x-ray tube for in vivo microtomography applications.