Objective To compare the accuracy of output factor calculation for rectangular inserts of electron beams by using three kinds of algorisms: square root, one dimensional formula and area periphery ration. Methods The differences between the values of output factor calculated by these three algorithms mentioned above and the results measured by ionization chamber for seven rectangular inserts were compared. Results When beam energy was fixed, the difference between calculated and measured output factors was larger for area periphery ration algorithm than that of the square root or one dimensional formula algorithms. The electron cone size, beam energy and rectangular inserts size all had some effect on the value of output factor calculated by the three algorithms. Conclusions The area periphery ration algorithm is not recommended for clinical use because of its great deviation. One dimensional formula and square root algorisms possess a good accuracy. One dimensional formula is superior to square root algorithm, but square root algorithm is more practical for clinical use.