The investigation of traditionally used medicinal plants is valuable both as a source of potential chemotherapeutic drugs and as a measure of safety for the continued use of these medicinal plants. Achillea millefolium L. (AM) is an ancient remedial herb native to Europe that is used to treat wounds, gastrointestinal and hepatobiliary disorders, inflammation, headaches, and pain. Bauhinia forficata Link (BF), an Asiatic plant, is one of the most commonly used plants in folk medicine against diabetes. The aim of this study was to evaluate the cytotoxic and antimutagenic potential of aqueous extracts of AM and BF on bone marrow cells of Wistar rats treated in vivo. These plant extracts possess considerable antioxidant activity due to the presence of flavonoids and phenolic compounds. These compounds were determinants to noncytotoxic and antimutagenic/protective action of these plants, that reduced statistically the percentage of chromosomal alterations induced by the chemotherapeutic agent cyclophosphamide in simultaneous (AM, 68%; BF, 91%), pre- (AM, 68%; BF, 71%), and post-treatment (AM, 67%; BF, 95%). Therefore, the results of this study indicate that extracts of A. millefolium and B. forficata have antimutagenic potential and that their consumption can benefit the health of those using them as an alternative therapy.