This research investigates the cytotoxic and genotoxic effects of the aqueous extract of Thymus vulgaris leaves. To study the cytogenotoxic effects of this plant, the impact of different concentrations (10 to 50 mg/ml) of its aqueous extract on the root growth, mitotic index, and the type and percentage of chromosomal abnormalities in the meristematic root cells of Allium cepa were examined. The results indicate that, overall, an increase in extract concentration led to a statistically significant decrease in root growth and mitotic index of meristematic cells in the onion roots. Moreover, all treatments except the negative control exhibited a percentage of various chromosomal abnormalities; although the increase or decrease was not concentration-dependent in the level of chromosomal abnormalities observed. Among these chromosomal abnormalities, c-mitosis, chromosomal breakage, and micronuclei were notable. This study suggests that the aqueous extract of Thymus vulgaris leaves may potentially have cytogenotoxic effects, emphasizing the need for cautious consideration in its usage.