Characterization of systemic performance of gold nanostructures is critical to the advancement of biomedical applications of these nanomaterials as imaging or therapeutic agents. The accuracy of current in vitro methods, however, is limited by interanimal variability. We present a novel method capable of monitoring the pharmacokinetics of PEGylated gold nanorods (GNRs) in the same animal by using intravital two-photon luminescence (TPL) imaging of GNRs flowing through a surface blood vessel. The TPL imaging with high speed and submicrometer resolution allowed for studying the clearance of GNRs as a function of surface coating. PEGylated-GNRs (PEG-NRs) were found to exhibit a biphasic clearance mode, with a significantly prolonged blood residence time for branched poly(ethylene glycol) (PEG) as compared to the linear PEG. With spectral detection to distinguish GNR TPL from tissue autofluorescence, we also mapped the cellular distribution of GNRs in the explanted organs, and found most GNRs resided in the macrophages in liver and spleen.