We report on the instrumentation development of a SPECT-CT system being configured at Johns Hopkins University to image the biodistribution of radiopharmaceuticals in unrestrained, unanesthetized mice. The gantry is a custom built x-ray computed tomography system based on the Siemens MicroCAT II imaging system. The x-ray system is composed of an 80 kVp (max), 4OW x-ray source and a 2048 × 3096-pixel detector (5-frames per second readout). The mouse will be anesthetized during the x-ray CT scan. SPECT imaging will be achieved using two low profile gamma cameras, 10 cm × 20 cm in size based on a 2×4 array of Hamamatsu H8500 (8×8 anode pads) flat panel position sensitive photomultiplier tubes (PSPMT). A NaI(Tl) scintillator array with 1.2 mm pitch is mounted to the PSPMT array. The front end readout electronics combine the anode outputs of the PSPMTs of the detector head. The data acquisition system is based on two CAEN 32 channel VME peak sensing analog-digital converter (ADC) modules per detector head to digitize the outputs. An infrared based animal position tracking system will be used to monitor the mouse's head position during a SPECT scan via infrared illuminated markers attached to the mouse's head. The mouse is confined in an infrared transparent burrow at the center of rotation of the gantry. The tracking system is able to track with sub-millimeter accuracy the mouse's head position at 10-15 frames per second.