Three-dimensional (3D) multi-modality imaging (MMI) is frequently used in human medicine but its use in equine diagnostic imaging has yet to be validated. In a proof of principle manner, this study aimed to evaluate 3D MMI co-registration of magnetic resonance (MR) and scintigraphic data for the assessment of equine foot injury. A multi-compartment equine foot phantom was designed and constructed using the Stereolithography Additive Manufacturing process. Images were obtained by MR imaging and by scintigraphy using different copper sulphate concentrations (CuSO4) (for MR imaging) or radiopharmaceutical concentrations (for scintigraphy) respectively, which were introduced into the compartments of the foot phantom to mimic the normal limb appearance for each image modality. Lesions at specific locations were simulated by introducing increased concentrations of CuSO4 or radiopharmaceutical into the appropriate compartments. 3D scintigraphic data was obtained by rotating the phantom through 360° with dynamic acquisitions performed every 3°. The MR and scintigraphy data were co-registered using proprietary software. MR image assessment showed the individual compartments of the phantom, and the location of a simulated lesion. The presence of increased radiopharmaceutical concentration was clear on scintigraphic images, but anatomical resolution was less clear than MR images. Accurate detection and localisation of simulated lesions were best with 3D co-registeration of the MR and scintigraphic images. In the future, 3D co-registration of scintigraphic and MR images may prove clinically useful to localise and differentiate between active and inactive injury. Issues relating to the practical implementation of 3D MMI in the standing sedated horse are discussed.