Integrated analytical techniques were used to study the tissue distribution and structural information of gold nanorods (Au NRs) in Sprague-Dawley rats through tail intravenous injection. Before in vivo experiments were conducted, careful characterization of Au NRs was performed. The zeta potential proved that adsorption of bovine serum albumin on Au NRs turned the surface charges from positive to negative as in an in vitro simulation. The biodistribution of Au NRs was investigated quantitatively by inductively coupled plasma mass spectrometry at different time points after injection. As target tissues, both liver and spleen were chosen to further demonstrate the intracellular localization of Au NRs by the combination of transmission electron microscopy and energy-dispersive X-ray spectroscopy. Moreover, synchrotron-radiation-based X-ray absorption spectroscopy was employed and it was observed that long-term retention of Au NRs in liver and spleen did not induce obvious changes in the oxidation states of gold. Therefore, the present systematic method can provide important information about the fates of Au NRs in vivo and can also be extended to study the biological effects of other metallic nanomaterials in the future.