Rotenone, Rhodamine 123, and Janus green B, inhibitors of mitochondria function, are currently investigated to create pharmacological agents that induce mitochondrial dysfunction and apoptosis. Since impaired mitochondrial function is associated with overproduction of reactive oxygen species, it seems relevant to compare DNA damage induced by the said inhibitors in Ehrlich ascites carcinoma cells and murine lymphocytic leukemia P388 and DNA damage induced by the direct effect of ionizing radiation (X-rays) that induces an increase of reactive oxygen species. The alkaline comet assay was used for measuring the level of DNA damage. The level of Rotenone-induced DNA damage was comparable to that one induced by very low-dose radiation (4 Gy) for both cell types. Post-irradiation incubation of cells led to a reduction in the level of DNA damage, indicating that damage to DNA is repaired. Treatment of Ehrlich ascites carcinoma cells with Rhodamine 123 and subsequent washing them for removal of excess dye did not cause an increase in the level of DNA damage, however, exposure to very low dose radiation (4 Gy) in the presence of Rhodamine 123 induced an increase in the level of DNA damage, which was significantly reduced after 1-hour incubation. It can be assumed that pre-treatment of cells with Rotenone or Rhodamine 123 that disrupt mitochondrial function contributed to the maintenance of the integrity of nuclear DNA in irradiated cells. Exposure to Janus green B caused an increase in the level of DNA damage and cell death. The alkaline comet assay revealed that damage induced by these compounds can be considered single- and double-strand breaks and alkali-labile (apurinic/apyrimidinic) sites in DNA.