Abstract: An ion implantation apparatus is provided with an ion source and a mass spectrometer having an analyzer magnet and is adapted to take out ions having a predetermined kinetic energy and mass from other ions produced in the ion source. It further includes a scanner system for scanning an ion beam of the take-out ions and irradiating the ion beam onto a substrate. The scanner system includes a deflection electro-magnet which is disposed downstream of the mass spectrometer for deflecting the ion beam in a predetermined plane with respect to a reference axis. A second vacuum chamber portion through which the ion beam passes in the magnetic field of the deflection electro-magnet is provided and a first vacuum chamber portion electrically independent of the second vacuum chamber portion is also provided through which the ion beam passes in the magnetic field of the mass analyzer. A third vacuum chamber portion is also provided through which the ion beam passes and in which the substrate is arranged for irradiation.