An electron beam exposure apparatus includes an electron beam generating section for generating a beam composed of electrons accelerated with a predetermined acceleration voltage, and a stage for mounting thereon a semiconductor wafer or reticle to be exposed by the electron beam. The stage includes a reference marker composed of a base section and a projection section. The base section is formed of a thin film of first conductive element having an atomic number greater than that of a material of the stage and has a first thickness through which more than 70% electrons in the beam can transmit and the projection section is formed of a bulk of second conductive element having an atomic number equal to or greater than that of the material of the stage and has a second thickness thicker than a maximum traveling distance of the electrons of the beam into the projection section. The electron beam exposure apparatus further includes an optical system for adjusting a deflection of the electron beam and a size of electron beam, and a detecting section for detecting electrons from the reference marker of the stage when the electron beam is irradiated on the reference marker of the stage in a calibration mode.