BACKGROUND We aimed to investigate the effects of (12)C(6+) irradiation on the cell cycle and apoptosis as well as the associated mechanisms in the human lung cancer cell line H1299. METHODS After irradiation with different doses of (12)C(6+) for varying lengths of incubation, the changes in H1299 cells were assayed by flow cytometry and the microculture tetrazolium test. The expression of caspase-3 was detected by immunocytochemistry, western blot, and reverse transcription-polymerase chain reaction (RT-PCR). RESULTS The G(2)/M phase was blocked after treatment with 1 and 2 Gy at the 12-hour time point, and the most obvious block of G(2)/M occurred after treatment with 2 and 4 Gy at the 24-hour time point in a dose-dependent manner. The apoptosis rate increased with increasing radiation dose and reached a peak after the cells were irradiated with 2 Gy and incubated for 48 hours. In addition, the RT-PCR, western blot, and ICC results showed that irradiation with (12)C(6+) significantly increased the expression of caspase-3 compared with the control group (p<0.05). CONCLUSIONS Irradiation of H1299 cells with (12)C(6+) induced apoptosis and significantly inhibited their growth through heavy ion irradiation-mediated activation of the caspase-3 pathway. Our results show that caspase-3 may play an important role in radiation-induced apoptosis through a p53-independent pathway.