Pinoxaden is the one of the acetyl-CoA carboxylases (ACCase) inhibiting herbicides and used for controlling grass weeds. In this study, cyto-genotoxic effects of Pinoxaden on the Allium cepa roots were investigated using Allium ana-telophase and comet assays by determining the root growth, mitotic index (MI), mitotic phases, chromosomal aberrations (CAs) and DNA damage. Different concentrations of Pinoxaden from 0.5 to 100 mg/L were employed on root tips for 96 h to find the effective concentration that reduces root tip elongation by 50% in comparison with negative control (EC50). Pinoxaden concentrations of 1.25 mg/L (1/2xEC50), 2.5 mg/L (EC50) and 5 mg/L (2xEC50); methyl methane sulphonate (MMS, 10 mg/L) for positive control and distilled water for negative control were exposed to Allium bulbs for several time intervals (24, 48, 72 and 96 h). Pinoxaden showed cytotoxic effects by decreasing the root growth and MI. Pinoxaden induced CAs including disturbed ana-telophase, anaphase bridges, chromosome laggards, stickiness, polyploidy, micronucleus at 5 mg/L, c-metaphase and binuclear cells and also DNA damage compared with control group. The current study confirmed cyto-genotoxic effects of Pinoxaden. Further research is needed to clarify the cyto-genotoxic mechanisms of Pinoxaden at molecular level.