We present a novel facility for micro-irradiation of living targets with ions from a 1.7 MV tandem accelerator. We show results using 1 MeV protons and 2 MeV He(2+). In contrast to common micro-irradiation facilities, which use electromagnetic or electrostatic focusing and specially designed vacuum windows, we employ a tapered glass capillary with a thin end window, made from polystyrene with a thickness of 1-2 μm, for ion focusing and extraction. The capillary is connected to a beamline tilted vertically by 45°, which allows for easy immersion of the extracted ions into liquid environment within a standard cell culture dish. An inverted microscope is used for simultaneously observing the samples as well as the capillary tip, while a stage-top incubator provides an appropriate environment for the samples. Furthermore, our setup allows to target volumes in cells within a μm(3) resolution, while monitoring the target in real time during and after irradiation.