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Recently, the Cracow ion microprobe has found its new application as a single ion hit facility (SIHF), allowing precise irradiations of living cells by a controlled number of ions. The instrument enables a broad field of research, such as survival studies, adaptive response investigations, bystander effect, inverse dose-rate effect, low-dose hypersensitivity, etc. This work presents principles of construction and operation of the SIHF based on the Cracow microprobe. We discuss some crucial features of optical, positioning, and blanking systems, including self-developed software responsible for semiautomatic cell recognition, for precise positioning of cells, and for controlling the irradiation process. We also show some tests carried out to determine the efficiency of the whole system and of its segments. In addition, we present results of the first irradiation measurements performed with living cells.