The control of tick Rhipicephalus (Boophilus) microplus, that has the cattle as preferential host, has been performed using products based on different chemical substances. However, the indiscriminate use of these products has caused the selection of resistant populations and damages to the environment, contaminating the soil and water. Tickcides, like fipronil (synthetic chemical) and thymol (natural chemical), are applied on cattle through aspersion, causing the death of the ectoparasites. Nevertheless, the effects of these products on nontarget organisms have not been thoroughly investigated. Thus, this study evaluated the morphology of the liver and thyroid of female Mus musculus mice, divided into 5 treatment groups/5 individuals each, exposed to fipronil (2%) and thymol (2 mg/mL) through aspersion baths. After exposure, the mice were euthanized with anaesthetic overdose and dissected for organ removal. The results showed that both fipronil and thymol caused morphological alterations in the organs: cytoplasmic vacuolation, cell death characteristics in hepatocyte nuclei and structural disorganization of the thyroid gland. Along with body weight measurement, the results suggest that the morphological alterations would be a systemic response of the organism to the toxic action of these products, regardless their origin (synthetic of natural).