An ion implanter includes an implantation chamber into which an ion beam is introduced, a holder for holding substrates on two columns of a first column and a second column in an X-direction, and a holder driving unit having a function of setting the holder in a horizontal state and then positioning the holder in a substrate exchange position and a function of setting the holder in a standing state and then driving reciprocally and linearly the holder along the X-direction in an irradiation area of the ion beam. Also, the ion implanter includes two load lock mechanisms, and two substrate carrying units equipped with arms, which carry the substrates between the load lock mechanisms and a substrate exchange position respectively, every two arms.