Nano-sized particles have received much attention in view of their varied application in a wide range of fields. For example, magnetite (Fe(3)O(4)) nanoparticles have been investigated for various medical applications. In this study, we visualized the distribution of administered magnetic nanoparticles in mice using both X-ray scanning analytical microscopy (XSAM) and magnetic resonance imaging (MRI). After administration, the nanoparticles were rapidly dispersed via the blood circulation, and reached the liver, kidney and spleen. Using the XSAM and MRI methods in a complementary fashion, the biodistribution of nano-sized magnetite particles was successfully visualized.