Quantum dots (QDs) are a novel class of inorganic fluorophores which are gaining widespread recognition as a result of their exceptional photophysical properties and their applications as a biomarker and in molecular biomedical imaging. The aim of this study was to evaluate the in vivo genotoxicity in mice exposed to CdSe quantum dots of average size 5.0 ± 0.2 nm and CdSe doped with 1% cobalt ions of similar size. The quantum dots are surface modified using mercaptoacetic acid (MAA) in order to be biocompatible and water-soluble. The MAA-QDs were given to the mice orally at doses of 500, 1000, and 2000 mg/kg by weight of MAA-QDs. Bone marrow and liver samples were collected after two and seven days of treatment. The results indicated that after two days of treatment, the high dose of doped MAA-QDs was significantly able to induce DNA damage, formation of micronuclei (MNs), and generation of DNA adduct (8-hydroxy-2-deoxyguanosine, 8-OHdG). However, increasing DNA damage and the frequency of MNs formation as well as the generation of DNA adducts were observed with both the undoped MAA-QDs (2000 mg/kg) and doped MAA-QDs (1000 and 2000 mg/kg) after seven days of treatment. The results of our study indicate that exposure to high doses of pure MAA-QDs or MAA-QDs doped with cobalt has the potential to cause indirect in vivo genetic damage, which may be attributed to free radical-induced oxidative stress in mice.