Abstract A microbeam line for analysis with adjustable objective slits and a magnetic quadrupole doublet was designed and installed in a beam line connected with a medium-current ion implanter (Disktron accelerator) with an energy of 500 keV. The dependence of excitation currents and rotational misalignments for each of the magnets on the final beam spot size was investigated. The results were compared with those estimated by a Monte Carlo procedure for the final beam spot profile. A minimum beam spot size of 0.7 μm × 0.9 μm for 400 keV helium ion beams was obtained. A typical beam current was 100 pA for a spot size of 1 μm × 1 μm. Secondary-electron and RBS mapping images using the microprobe with 400 keV helium ions were obtained.