Biological research in recent years has generated significant interest for in vivo small animal imaging technologies. 3D small animal X-ray computed tomography (CT) provides anatomical images with high spatial resolution and good bone-to-soft tissue contrast. Radiation doses to the subject can be significant when soft tissue contrast and high-resolution images are desired. We have used the MCNP Monte Carlo simulation, and calibrated thermoluminescent dosimeters (TLD's), in combination with high resolution X-ray spectra obtained with a cadmium zinc telluride (CZT) detector, to calculate the depth dependent dose in 3D high resolution X-ray CT. Three spectra (30 kVp with 0.25 mm of aluminum filtration, 40 kVp with 0.50 mm Al, and 50 kVp with 1.00 mm Al) were chosen as representative of soft, medium, and hard beams. MCNP was used to simulate the dose from these X-ray spectra incident upon a cylindrical mouse-sized phantom (2.54×6.1cm). The same phantom was also constructed from solid lucite material with thermo-luminescent dosimeters (TLD's) placed at the positions where we sampled the dose with MCNP. The maximum and minimum dose observed in this study is 19.7 ± 1.7 cGy from the soft beam measured nearest the surface, and 5.2 ± 0.1 cGy from the hard beam measured furthest from the source, for a typical data acquisition with 196 angles.