It is well-known that the DNA damage caused by charged particles considerably differs from damage due to electromagnetic radiation. In the case of irradiation by charged particles the DNA lesions are more complex and clustered. Such clustered damage is presumed difficult to be repaired, and is potentially lethal. In this study, we utilize a 90°-scattering system and related imaging techniques to investigate the accumulation of γ-H2AX along the trajectory of charged particles. By immunostaining the γ-H2AX protein, optical images of corresponding double strand breaks were observed using a high resolution confocal microscope. We demonstrate the difference in the accumulation of γ-H2AX from irradiation by 1 MeV protons and that of 150 keV X-rays. The acquired images were arranged and reconstructed into a 3D image using ImageJ software. We discovered that the γ-H2AX foci, following irradiation by protons, have a tendency to extend in the beam direction, while those from X-ray irradiation tend to be smaller and more randomly distributed. These results can be explained by the physical model of energy deposition.