Flexible approaches to defining microvessel morphometry are useful in the study of both acute and chronic structural changes of the microcirculation. In this report, we examined the utility of the intravascular infusion of lipophilic carbocyanine tracers in the structural assessment of the retina, skin, lung, and colon microcirculation. The microvessel labeling technique, here termed fluorescent vessel painting, involved the intravascular injection of sulfonated lipophilic carbocyanine tracers. The utility of vessel painting in morphometry was assessed using morphometric comparisons with corrosion casting and 2-dimensional and 3-dimensional scanning electron microscopy. The comparisons demonstrated that fluorescent vessel painting modestly overestimated the interbranch angles, interbranch distances, and vessel diameters of the 2D mucosal plexus of the colon. These differences were narrowed with the application of confocal microscopy. The advantages of fluorescence vessel painting included (1) the filling of all tissues including the relatively high resistance microvessels of the mouse skin, (2) the ability to use tissue counterstains such as DAPI, and (3) the prolonged stability of the lipophilic tracer after aldehyde fixation. These studies suggest the utility of fluorescent vessel painting as a complementary technique to corrosion casting in the morphometric study of the microcirculation.