In this study, we aimed to use gold nanorods (Au-NRs) as luminescent substrates for labeling of the mouse intestinal blood vessels for tissue imaging. The labeled intestine was subjected to 3-D confocal microscopy to reveal the intricate morphology of the intestinal capillaries. Using the Au-NR's unique near-infrared excitation and visible fluorescence emission, we observed low noise background compared to the tissue's high autofluorescence from blue laser excitation. We took advantage of this sharp contrast in optical properties to achieve 3-D visualization of the intestinal microstructure and vasculature with capillary-level resolution. This new optical application demonstrates the Au-NR's distinctive properties in vascular labeling and fluorescence microscopy for 3-D illustration of intestinal vasculature.