The accumulation of lead (Pb), cadmium (Cd), nickel (Ni), iron (Fe), copper (Cu), and zinc (Zn) in the femora of four rodent species (Apodemus flavicollis, Apodemus sylvaticus, Myodes glareolus, and Microtus arvalis) trapped at different polluted areas in Slovakia (Kolíňany and Nováky) was investigated in the present study. We detected the highest concentration of Pb in bones of A. sylvaticus from both polluted areas; however, no significant changes between species were observed. In the femora of M. glareolus, the highest concentrations of Cd, Ni, and Zn were detected at both areas. Significant differences were observed between A. flavicollis and M. glareolus, M. glareolus and M. arvalis (for Cd concentration); and between M. glareolus and remaining species (for Zn concentration). The highest concentration of Fe was found in bones of A. flavicollis and M. glareolus from Nováky and Kolíňany areas, respectively. Significant differences (for Ni, Fe, and Cu concentrations) were examined between A. flavicollis and A. sylvaticus, A. flavicollis and M. arvalis. Although the highest concentration of Cu was found in bones of M. glareolus and A. flavicollis from Nováky and Kolíňany areas, respectively, no significant differences between species were observed. Our results demonstrate increased accumulation of some heavy metals (mainly Cd, Fe, Pb, and Zn) in the femora of small mammals from both polluted areas in Slovakia in comparison with other polluted biotopes in Europe and thus provide evidence of intensive environmental contamination. M. glareolus may be considered the most loaded zoomonitor with heavy metal contamination as compared to other species.