Iron oxide magnetic nanoparticles (MNPs) are widely used as diagnostic and therapeutic agents for biomedical applications. Quantitatively analyzing biodistribution, pharmacokinetics and organ clearance of MNPs in mouse models is important for understanding their in vivo behavior. In this study, we developed a novel histochemical method for visualizing unlabeled MNPs in mouse tissues by employing their intrinsic peroxidase-mimicking activity, regarding which we reported previously that MNPs could catalyze the oxidation of peroxidase substrates to produce a color reaction at the site of MNPs (Gao et al. Nat. Nanotechnol.2007, 2, 577-583). Based on this MNPs-peroxidase approach, we determined the biodistribution and organ clearance of MNPs by visualizing and quantifying the localization of MNPs within the main organs. Compared to traditional Prussian blue assay, this novel MNPs-peroxidase approach has higher sensitivity. In conclusion, the developed MNPs-peroxidase approach based on intrinsic peroxidase activity of iron oxide nanoparticles was used effectively for quantitative detection of MNPs in mice by histochemical staining. Presumably, other nanoparticles having intrinsic peroxidase activity could also be considered.