Substances added to food are considerable for survival and are the oldest technologies used in preservation, sweetening and coloring. This work was conducted to evaluate the toxicity of the food additives sunset yellow (SY) and brilliant blue (BB) on Allium cepa root meristematic cells. Control and treatment groups were created from germinated roots. Group 1 (control group) did not receive chemicals. Group 2 (SY or BB-treatment group), received increasing doses of SY (25, 50, 100 and 500 ppm) and BB (100, 200, 400 and 500 ppm) with time periods of 24, 48 and 72 h. After different treatment periods, the roots were obtained from all groups and EC50 concentrations, cell death, chromosome aberrations, mitotic index were observed by a light microscopy. Changing antioxidant capacity of roots was determined by FRAP and TEAC assay. Also, DNA damage was measured by comet assay and RAPD-PCR technique. Approximately 50 and 200 ppm were accepted as EC50 value for SY and BB, respectively. Chromosome aberration values were obtained with increasing concentrations and longer treatment times such as chromosome bridge, C-mitosis, micronucleus, chromosome mis-segregation in both groups. Increasing exposure doses of SY and BB caused decreasing mitotic index values at 72 h. FRAP and TEAC assay showed that antioxidant capacity of roots was decreased by increasing concentrations of SY and BB. The tail DNA% and tail length significantly increased for all exposure times when compared to the control group. 50 and 200 ppm of SY and BB caused a genotoxic effect on genetic material at 72 h according to RAPD-PCR. Increasing the doses of SY and BB resulted in increased toxicity to all studied parameters of A. cepa. In conclusion, the SY and BB tested in this study have cytotoxic and mutagenic potential. Furthermore, SY is more harmful than BB for use in the A. cepa root meristematic cells.