Multi-leaf collimators (MLCs) are used in image guided radiation therapy to shape the radiation beam as it is traveling around a patient. In order to do this, metal leaves open and close, allowing radiation to pass or blocking it as the radiation source moves. The path of the beam and the shape of the collimation are optimized by treatment planning software to maximize the dose to tumors while minimizing the dose given to the patient. This type of therapy represented a major step forward in the treatment of many types of tumors. However, preclinical studies of small animals are not performed under the same conditions. In order for the results of this type of basic research to be applied to the clinic accurately, tools like MLCs need to be developed but on a much smaller scale for small animal studies. This is the design of such an MLC, dubbed a binary micro MLC (bmMLC). All the computer-aided design (CAD) files are here for download and can then be manufactured or modified. The bmMLC presented here represents the smallest MLC constructed to date and is capable of administering a radiation beam that can be modulated by 1 mm increments. It can be used to perform much more accurate studies of guided therapy on small animal models.