In the near future, nanotechnology is envisaged for large-scale use. Hence health and safety issues of nanoparticles (NPs) should be promptly addressed. Twenty-eight-day oral toxicity, genotoxicity, biochemical alterations, histopathological changes and tissue distribution of nano and microparticles (MPs) of manganese oxide (MnO2) in Wistar rats was studied. Genotoxicity was assessed using comet, micronucleus and chromosomal aberration assays. The results demonstrated a significant increase in DNA damage in leukocytes, micronuclei and chromosomal aberrations in bone marrow cells after exposure of MnO2-NPs at 1000, 300 mg kg–1 bw per day and MnO2-MPs at the dose of 1000 mg kg–1 bw per day. Our findings showed acetylcholinestrase inhibition at 1000 as well as at 300 mg kg–1 bw per day in blood and with all the doses in the brain indicating the toxicity of MnO2-NPs. Further, the doses significantly inhibited different ATPases in the brain P2 fraction. Significant changes were observed in aspartate aminotransferase (AST), alanine aminotransferase (ALT) and lactate dehydrogenase (LDH) in the liver, kidney and serum in a dose-dependent manner. MnO2-MPs at 1000 mg kg–1 bw per day were found to induce significant alterations in biochemical enzymes. A significant distribution was found in all the tissues in a dose-dependent manner. MnO2-NPs showed a much higher absorptivity and tissue distribution as compared with MnO2-MPs. A large fraction of MnO2-NPs and MnO2-MPs was cleared by urine and feces. Histopathological analysis revealed that MnO2-NPs caused alterations in liver, spleen, kidney and brain. The MnO2-NPs induced toxicity at lower doses compared with MnO2-MPs. Further, this study did not display gender differences after exposure to MnO2-NPs and MnO2-MPs. Therefore, the results suggested that prolonged exposure to MnO2 has the potential to cause genetic damage, biochemical alterations and histological changes. Copyright © 2013 John Wiley & Sons, Ltd.