The visual system is vital to human health, and the effects of ionizing radiation on vision have received increasing attention. Using a zebrafish model, this study was designed to investigate the apoptosis in eyes induced by carbonion irradiation. Zebrafish embryos at 12 h post-fertilization (hpf) were irradiated using 12C6+ion beams at doses of 2, 4 and 8 Gy.