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Tropaeolum majus L. (Tropaeolaceae), commonly known as nasturtium, is an important edible plant native to the Andean States and widely disseminated throughout South America. Despite the use of this species is quite widespread, there are no minimum quality control standards or data on its genotoxicity. So, the aim of this study was to present a detailed anatomical and histochemical study for Tropaeolum majus and provide genotoxicity parameters of a preparation routinely used in South American countries. First, three different Tropaeolum majus aqueous extracts (TMAEs) at concentrations of 1.5%, 7%, and 15% were prepared according to the popular use. Then, genetic toxicity of TMAE was evaluated on bacterial reverse mutation, genomic lesions, and micronucleus formation in male rats. Furthermore, a detailed anatomical and histochemical study of the leaves and stems of Tropaeolum majus were performed. No revertant colonies were found in any bacterial cultures examined. In the comet assay, TMAE showed no significant DNA damage in all tested doses. Micronucleus assay showed no significant increases in the frequency of inducing micronuclei in any dose examined. Light and electron microscope images of cross-section of leaves and stems from Tropaeolum majus revealed useful diagnostic features. The presented data showed significant safety parameters for the use of TMAE and provided important data for the quality control of this plant species.