The invention facilitates transport of an immobilized, anesthetized small animal across multiple single-modality or multiple-modality imaging workstations at the same or different physical locations without loss of subject positional information. The animal holder is compatible with preclinical animal imaging stations such as micro-CT, micro-MR, micro-PET, micro-SPECT, and FMT. The animal holder is configured to be accommodated by (for example, fit within) individual imaging chambers of such instruments and is fabricated from materials that are compliant with all of the imaging modalities used. In certain embodiments, an integrated set of fiducial marker wells accommodates the dispensing of markers that are picked up by several modalities simultaneously in multiple planes. The fiducial markers then are aligned in standard image processing or image analysis software with simple image translation and rotation operations, without the need for more advanced scaling, distortion or other operations. The animal holder optionally also includes a system for providing the animal with inhalation anesthesia, for example, isoflurane, and is designed to fit into identical receptacles inside or outside the imaging workstation(s) that provide heating to minimize or prevent animal hypothermia.