An automated single cell recognition and irradiation system has been developed at a high-energy heavy ion microbeam. The system has been installed on a vertical beam line of the JAERI Takasaki AVF-cyclotron accelerator to irradiate individual biological cells in an air environment with energies of more than 10 MeV/u by single ions. The system consists of high-precision stages, optical microscopes with CCD camera, a computer network and software packages to obtain positional data from a cluster of individual samples randomly placed on a holder before irradiation and to irradiate them with individual ions according to the obtained data. This paper will describe the new systems, and show results from irradiation experiments for CR-39.