Nano-materials are expected to be used for medical applications such as research on pharmacokinetics and novel therapeutic agents. Their acute toxicity should be examined and systemic distribution of the nano-materials should also be estimated. We established a high resolution in vivo 3D microscopic system for a novel fluorescence imaging method at single molecular level. We measured in vivo movement of CdSe nano-particles (quantum dots (QDs)) conjugated with monoclonal anti-HER2 antibody (Trastuzumab) in tumor vessel to breast cancer cells. The HER2 protein expressed in cancer cells and its in vivo dynamics were visualized by QDs at nano-scale. It suggests future utilization of the system to improve drug delivery system to target the primary and metastatic tumors for made to order treatment. We also describe a novel contrast medium for X-ray and its distribution in organs. Nano-sized silica coated silver iodide beads exhibited contrast enhancementin the tumor for over one hour. Sentinel node navigation is one of the important clinical applications for fluorescence nano-particles and silver iodide beads. Our experimental data of those nano-particles in experimental model have shown the potential of fluorescence and X-ray measurement to be alternatives to existing tracers. Future innovation in cancer imaging by nano-technology and novel measurement technology will provide great improvement, not only in clinical field of prevention, diagnosis and treatment of human disease, but also in basic medical science.