Ethnobotanical studies have investigated the use of leaves of Cunila microcephala for respiratory, stomach and gastrointestinal disorders. The essential oil of this plant is mostly composed of menthofuran, which has a hepatotoxic effect. Due to the popular use of this plant in southern Brazil, this study aimed to perform phytochemical profile of C. microcephala to detect and determine the amount of secondary metabolites and to evaluate their microbiological activity in vitro and genetic damage in vivo, indicative of genotoxicity, to ensure safe use of the plant. The leaf extract of C. microcephala was investigated for the presence of phenolic compounds, such as tannins, coumarins and flavonoids. This extract contained 193.23 mg/ml of phenolic compounds. In our in vitro analysis of microbiological activity, the crude leaf extract of C. microcephala showed 6 mm zone of inhibition against Staphylococcus aureus; fractions of dichloromethane and ethyl acetate showed 4 mm zones. In the genotoxic analysis, using the comet assay, no genotoxic effects were observed in blood samples and the liver at 125, 250 and 500 mg/kg. According to the results, C. microcephala presents interesting secondary compounds with biological activity, showing antimicrobial effects in vitro and no genotoxic effects in vivo.