Estimations of dog lung, pig heart, and pig kidney regional perfusion by use of fluorescent-labeled microspheres were compared with measurements obtained with standard radiolabeled microspheres. Pairs of radio- and fluorescent-labeled microspheres (15 microns diam, 6 colors) were injected into a central vein of a supine anesthetized dog and the left ventricle of three supine anesthetized pigs while reference blood samples were simultaneously withdrawn from a femoral artery in the pigs. The lungs were cubed into approximately 2 cm3 pieces (n = 1,510). Each pig heart and kidney was cubed into approximately 1-g pieces (total n = 192 and 120, respectively). The radioactivity of each organ piece and reference blood sample was determined using a scintillation counter with count rates corrected for decay, background, and spillover. Tissue samples and reference blood samples were digested with KOH and filtered and the fluorescent dye was extracted with a solvent, or the dye was extracted from lung tissue without filtering. The fluorescence of each sample was determined for each color by use of an automated spectrophotometer. Perfusion was calculated for each organ piece from both the radioactivity and fluorescence. Correlation between flow determined by radio- and fluorescent-labeled microspheres was as follows: r = 0.96 +/- 0.01 (SD) (lung, filtered, n = 588), r = 0.99 +/- 0.00 (lung, nonfiltered, n = 710), r = 0.95 +/- 0.02 (heart, filtered), and r = 0.96 +/- 0.02 (kidney, filtered). Compared with colored microspheres, methods for quantitating fluorescent-labeled microspheres are more sensitive, less labor intensive, and less expensive. Fluorescent-labeled microspheres provide a new nonradioactive method for single and repeated measurement of regional organ perfusion.