An electron beam apparatus is provided for reliably measuring a potential contrast and the like at a high throughput in a simple structure. The electron beam apparatus for irradiating a sample, such as a wafer, formed with a pattern with an electron beam to evaluate the sample comprises an electron-optical column for accommodating an electron beam source, an objective lens, an E×B separator, and a secondary electron beam detector; a stage for holding the sample, and relatively moving the sample with respect to the electron-optical column; a working chamber for accommodating the stage and capable of controlling the interior thereof in a vacuum atmosphere; a loader for supplying a sample to the stage; a voltage applying mechanism for applying a voltage to the sample, and capable of applying at least two voltages to a lower electrode of the objective lens; and an alignment mechanism for measuring a direction in which dies are arranged on the sample. When the sample is evaluated, a direction in which the stage is moved is corrected to align with the direction in which the dies are arranged.