Feature sizes of recent semiconductor devices have reached the submicron level. Electron beam metrology uses a focused electron beam rather than an optical beam. Thus it can measure the submicron devices because of its very fine spot capability. Because this technology is newly developed, there are several uncertainties in this application. The main uncertainties are repeatability of measured length, or precision and absoluteness of the obtained value, accuracy. This paper discusses the repeatability of the newly developed electron beam metrological system. The system's features are explained, elements affecting repeatability are considered, and the experimental results are shown.