Despite the lack of knowledge of their exact effects, peloids (natural muds) are widely applied in clinical treatment and prevention of different diseases, especially in rheumatic and gynecological disorders or skin diseases. Primarily we have information on their inorganic components, but only limited data are available on the organic components and nothing on their mechanism of chemical action. The objective of the present study was to detect the DNA-damaging effects (possible genotoxic effect) of peloid samples using the single-cell comet assay on Long Evans rat lymphocytes, human lymphocytes, and Eisenia fetida coelomocytes. Rat and human lymphocytes were exposed to the in toto peloid samples, in vitro. The Eisenia cells were extracted from the coelom of animals kept in the intact peloid sample. An indicator derived from the DNA fluorescence intensity was used in the statistical evaluation. The predominantly organic (Hévíz) sample showed a significant alteration from the negative control in several cases, while the inorganic (Kolop) applied did not. A higher quantity of organic compounds may have an important role in the emergence of DNA damage. The results revealed that medical muds have not only positive health effects but can also contain substances with potential human toxicity risk. Our research provides essential steps towards the creation of a toxicity profile and the possible safe use of peloids as medicinal therapy.