In this study, the toxic effects of epiclorohidrine (ECh) were investigated in vivo by Allium test. The toxic effects have been investigated in terms of physiological, cytogenetic, anatomical, and biochemical aspects. The changes in germination percentage, weight gain, and root length were investigated as physiological parameter; micronucleus (MN), mitotic index (MI), and chromosomal abnormality (CA) frequencies were as cytogenetic parameter. Oxidative stress indicators such as superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA) were analyzed for biochemical changes and also damages in root tip cells were evaluated as anatomical parameter. It was determined that germination percentage, weight gain, root length, and MI decreased; MN and CA frequencies were increased with the increase of ECh treatment dose. ECh treatment caused significant increase in SOD and CAT enzyme activities and MDA levels and these results indicated a stress formation. A variety of anatomical changes and damages were observed in the root tip cells induced by ECh. In conclusion, the toxic effects of ECh on A. cepa which is a model of eucaryotic cell were investigated in a multi-directional way and serious toxic effects of ECh treatment were determined.