In this study, the toxicity of epichlorohydrin, a chemical intermediate, was investigated by using Allium cepa L. test material as a bio-indicator. In addition, the protective role of sage leaf extract (Slex) against this toxicity was investigated. Toxicity was handled with the help of physiological (germination percentage, root elongation, and weight gain), cytogenetic (mitotic index = MI, micronucleus = MN, and chromosomal abnormalities = CAs), biochemical (malondialdehyde = MDA, superoxide dismutase = SOD, and catalase = CAT), and anatomical (root meristem cell damages) parameters. A. cepa bulbs were divided into 6 groups (1 control, 5 applications). The bulbs in the control group were treated with tap water, and the bulbs in the application group were treated with epichlorohydrin at a dose of 100 mg/L and Slex at two different doses (190 mg/L and 380 mg/L) and germinated. Germination process was continued uninterruptedly for 72 h in all groups. At the end of the period, physiological parameter measurements were carried out in the bulbs. In addition, root tips were collected and made ready for cytogenetic, biochemical, and anatomical measurements and microscopic observations. As a result, exposure to epichlorohydrin caused statistically significant (p < 0.05) decreases in germination percentage, root length, weight gain, and MI, and statistically significant (p<0.05) increases in MN frequency, CA numbers, MDA level, SOD, and CAT enzyme activities. Epichlorohydrin exposure induced CAs such as fragment, sticky chromosome, unequal distribution of chromatin, reverse polarization, and disordered mitosis in root meristem cells. The toxicity of epichlorohydrin was due to its interaction with DNA, and this interaction was confirmed by the spectral shift in the DNA spectrum. In addition, epichlorohydrin caused anatomical damages such as epidermis cell damage, cortex cell damage, thickening of the cortex cell wall, and flattened cell nuclei in root meristem cells. The application of Slex together with epichlorohydrin decreased the toxicity of epichlorohydrin and again caused statistically significant (p < 0.05) improvements in the values of all the parameters examined. In other words, germination percentage, root length, weight gain, and MI increased again and MN frequency, CAs numbers, MDA level, SOD, and CAT enzyme activities decreased. It was determined that this improvement was even more pronounced at 380 mg/L dose of Slex. As a result, it was determined that epichlorohydrin caused multiple-toxicity for the investigated indicator organism, and Slex had a reducing role in this toxicity. For this reason, Slex should be included in the daily diet as an antioxidant beverage in order to protect from the toxicity of chemical agents exposed in daily life or to reduce their effects.