We compared the effects of animal gender, species, and intestinal helminth burden on mercury concentrations in rodents. Total mercury concentrations were determined in the liver and kidney tissues of 80 small rodents (44 yellow-necked mice, Apodemus flavicollis, and 36 bank voles, Myodes glareolus) captured in the Ore Mountains (northwest Bohemia, Czech Republic). Overall, 25/80 (32%) of animals were infected by intestinal helminths. The differences in mercury concentration between rodents infected and not infected with intestinal helminths were not statistically significant. Statistically significant differences in mercury concentrations were found only between voles and mice (that were not infected with intestinal helminths). This suggests the differences may be associated with host genetics. Apodemus flavicollis body tissues had significantly lower (P=0.01) mean Hg concentrations (0.032 mg/kg) than Myodes glareolus (0.279 mg/kg), provided that animals were not infected by intestinal helminths; if the animals were infected by intestinal helminths, the difference between both groups was insignificant. The effect of gender in this study was significant only for voles (without helminth infection); for mice (either with or without helminth infection) the differences between genders were not significant. Myodes glareolus males had significantly lower (P=0.03) Hg concentrations in liver and kidney tissues (0.050 mg/kg) than Myodes glareolus females (0.122 mg/kg). These results reveal the importance of considering species and gender when evaluating mercury concentrations.