In the present study, toxic effects of glyphosate on Allium cepa L. (Amaryllidaceae) cells were investigated. For this aim, we used the germination percentage, root length, seedling weight, malondialdehyde (MDA) level, frequency of micronucleus (MN), chromosomal aberrations (CAs) and mitotic index (MI) as indicators of toxicity. In addition to the analyses mentioned above, we also examined changes in the root anatomy of A. cepa seeds treated with glyphosate. Glyphosate was applied with three different doses (100, 250 and 500 mg l(-1)). The results showed significant alterations in the germination percentage, root length, seedling weight, MDA level, MN, CAs and MI frequency depending on treatment doses in the glyphosate treated groups. Glyphosate-exposure significantly reduced the germination percentage, root length and seedling weight in all the treatment groups (P<0.05). But, an increase in the MN and CAs formation (P<0.05) was observed. It was also found that glyphosate has a mitodepressive action on mitosis, and the MI was decreased depending on the dose of applied-glyphosate (P<0.05). Besides, 100, 250 and 500 mg l(-1) doses of glyphosate significantly enhanced the lipid peroxidation and caused an increase in malondialdehyde (MDA) levels at each dose treatment (P<0.05). Moreover, light micrographs showed anatomical damages such as unclear vascular tissue, unclear epidermis layer, cell deformation, unusual form of cell nucleus (usually flat) and binuclear cells. Each dose of glyphosate caused severe toxic effects on A. cepa cells and the strongest toxic effect was observed at the dose level of 500 mg l(-1).