Small animal in vivo anatomical (microCT and microMRI) and functional (microSPECT and microPET) imaging has fostered the development of radiopharmaceuticals and fundamental cancer research. Similar advances in the fields of radiobiology, radiotherapy planning, radiosensitizers, and radiation therapy are anticipated if dedicated small animal micro-conformal irradiation instruments are developed. We are presenting the design of a small animal image guided microirradiator (microIGRT) based on a high resolution microCT for anatomical imaging and treatment planning and a submillimeter focal spot orthovoltage source for high resolution conformal microirradiation. Each of the subsystems, the microCT and the microirradiator (microRT), have separate gantries which are placed in a coaxial instrument architecture. The on board microCT subsystem is a cone beam imaging tomographic scanner designed using a micro focus x-ray source and a flat panel amorphous silicon detector. The microRT subsystem was designed using an orthovoltage 320kVp x-ray source. Each subsystem is sequentially operated and a motorized animal bed transfers the small animal from the microCT imaging subsystem to the microRT subsystem. Treatment planning is performed during the transfer of the small animal by using an in house developed treatment planning. In this article, we report the design of the system and simulations performed to test the performance of our design.