Environmental contamination with cadmium (Cd) and fluorine (F) and the associated health impacts on humans have raised significant concerns in the literature, but the additional health risks created by Cd have not been investigated in areas with endemic fluorine intoxication (fluorosis). Here, we report for the first time that naturally occurring Cd in areas where endemicfluorosis is related to coal combustion is a serious hidden toxin. The high Cd levels in rocks and soils of these areas may increase health risks to epidemiological level, irrespective of fluorine levels. We implemented a pilot study in a fluorosis-affected rural area within China’s Three Gorges region, and revealed enrichment of Cd in local bedrock (4.48-187 mgkg(-1)), coal (11.5-53.4 mgkg(-1)), and arable soils (1.01-59.7 mgkg(-1)). Cadmium was also observed to concentrate in local food crops (0.58-14.9 mgkg(-1)) and in the urine of local residents (1.7-13.4 microgL(-1)). A routine epidemiological investigation revealed that the two major Cd exposure pathways were through crop consumption and inhalation of emissions from coal combustion. Therefore, the naturally occurring Cd in areas with endemic fluorosis related to coal combustion represents a previously unrecognized toxin that must be addressed as part of efforts to control the endemic problem. The biogeochemical processes of Cd and the associated environmental effects will require additional in-depth study.