A method and system for automatically conditioning a linear accelerator is disclosed. The method and system comprise the steps of measuring the global variables of the accelerator and evaluating a plurality of events based upon the measurement of the global variables in which the plurality of events have a hierarchy of importance. Finally, the method and system includes performing an action in response to the hierarchy of importance of the plurality of events. Accordingly, a system and method in accordance with the present invention allows an accelerator to be conditioned unattended. The system and method in accordance with the present invention combines software and hardware to measure global variables and modifies the condition of the accelerator based upon those variables. Through the use of a system and method in accordance with the present invention conditioning can proceed in small systematic steps, thereby resulting in better-conditioned accelerators. Accordingly, an improvement in both the performance and longevity of the accelerator will result due to the reduction in arcing and dark current. Additionally, a complete record of the conditioning process is automatically generated and archived with the attending benefit of quality control. Finally a significant savings in the overall costs will result from the utilization of a system and method in accordance with the present invention.