To develop a silicon (Si) and cadmium telluride (CdTe) imaging Compton camera for biomedical application on the basis of technologies used for astrophysical observation and to test its capacity to perform three-dimensional (3D) imaging. All animal experiments were performed according to the Animal Care and Experimentation Committee (Gunma University, Maebashi, Japan). Flourine 18 fluorodeoxyglucose (FDG), iodine 131 ((131)I) methylnorcholestenol, and gallium 67 ((67)Ga) citrate, separately compacted into micro tubes, were inserted subcutaneously into a Wistar rat, and the distribution of the radioisotope compounds was determined with 3D imaging by using the Compton camera after the rat was sacrificed (ex vivo model). In a separate experiment, indium 111((111)In) chloride and (131)I-methylnorcholestenol were injected into a rat intravenously, and copper 64 ((64)Cu) chloride was administered into the stomach orally just before imaging. The isotope distributions were determined with 3D imaging after sacrifice by means of the list-mode-expectation-maximizing-maximum-likelihood method. The Si/CdTe Compton camera demonstrated its 3D multinuclear imaging capability by separating out the distributions of FDG, (131)I-methylnorcholestenol, and (67)Ga-citrate clearly in a test-tube-implanted ex vivo model. In the more physiologic model with tail vein injection prior to sacrifice, the distributions of (131)I-methylnorcholestenol and (64)Cu-chloride were demonstrated with 3D imaging, and the difference in distribution of the two isotopes was successfully imaged although the accumulation on the image of (111)In-chloride was difficult to visualize because of blurring at the low-energy region. The Si/CdTe Compton camera clearly resolved the distribution of multiple isotopes in 3D imaging and simultaneously in the ex vivo model.