An integrated microtomography and optical imaging system includes a rotating table that supports an imaging object, an optical stage, and separate optical and microtomography imaging systems. The table rotates the imaging object about a vertical axis running therethrough to a plurality of different rotational positions during a combined microtomography and optical imaging process. The optical stage can be a trans-illumination, epi-illumination or bioluminescent stage. The optical imaging system includes a camera positioned vertically above the imaging object. The microtomography system includes an x-ray source positioned horizontally with respect to the imaging object. Optical and x-ray images are both obtained while the imaging object remains in place on the rotating table. The stage and table are included within an imaging chamber, and all components are included within a portable cabinet. Multiple imaging objects can be imaged simultaneously, and side mirrors can provide side views of the object to the overhead camera.