Breast cancer patients are treated intraoperatively with radiation shortly after excision of a tumor. Pathology of the tissue is determined with a nearly instantaneous method, further excision is performed if needed, and the patient, still anesthetized and preferably unmoved, is then treated with radiation therapy. In a preferred embodiment an applicator is inserted into the excision cavity, the cavity is three-dimensionally mapped using radiation sources and a sensor, a radiation treatment plan is developed using a radiation prescription and the determined shape and location of the cavity, and the treatment plan is executed, all while the patient remains under anesthesia.