We investigated the radiation-quality-dependent bystander cellular effects using heavy-ion microbeams with different ion species. The heavy-ion microbeams were produced in Takasaki Ion Accelerators for Advanced Radiation Application, National Institutes for Quantum Science and Technology. Carbon (12C5+, 220MeV), neon (20Ne7+, 260MeV) and argon (40Ar13+, 460MeV) ions were used as the microbeams, collimating the beam size with a diameter of 20μm. After 0.5and 3h of irradiation, the surviving fractions (SFs) are significantly lower in cells irradiated with carbon ions without a gap-junction inhibitor than those irradiated with the inhibitor. However, the same SFs with no cell killing were found with and without the inhibitor at 24h. Conversely, no cell-killing effect was observed in argon-ion-irradiated cells at 0.5 and 3h; however, significantly low SFs were found at 24h with and without the inhibitor, and the effect was suppressed using vitamin C and not dimethyl sulfoxide. The mutation frequency (MF) in cells irradiated with carbon ions was 8- to 6-fold higher than that in the unirradiated control at 0.5 and 3h; however, no mutation was observed in cells treated with the gap-junction inhibitor. At 24h, the MFs induced by each ion source were 3- to 5-fold higher and the same with and without the inhibitor. These findings suggest that the bystander cellular effects depend on the biological endpoints, ion species and time after microbeam irradiations with different pathways.