BACKGROUND. The use of radioactive microspheres (RM) for the measurement of regional myocardial blood flow (RMBF) is limited and inaccessible to many investigators due to radiation safety concerns and radioactive waste disposal problems. Therefore, a new method for the measurement of RMBF using colored microspheres (CM) was developed. METHODS AND RESULTS. Polystyrene spheres (diameter, 15 +/- 0.1 [SD] micron; density, 1.09 g/ml) were dyed with one of five colors. With the injection of CM into the left atrium or into a coronary perfusion line, RMBF and its distribution can be determined. CM are extracted from the myocardium and blood by digestion with potassium hydroxide and subsequent microfiltration. The dyes are then recovered from the CM within a defined volume of a solvent, and their concentrations are determined by spectrophotometry. The separation of composite absorbance spectra by spectrophotometry with the CM technique was as good as the separation of energy spectra by a gamma-counter using the RM technique. Leaching of dye from the CM was less than 0.1% during a 2-month period in vitro. Significant leaching of dye from the microspheres also did not occur during 8 hours in the blood and myocardium of four anesthetized dogs in vivo. For further validation of this method, pairs of CM and RM (15.5 +/- 0.1 [SD] microns) were simultaneously injected under five different RMBF conditions (range, 0-10 ml/[min.g]) into the left anterior descending coronary artery of four anesthetized pigs, with coronary inflow as a flow reference, or into the left atrium of four anesthetized dogs using aortic blood withdrawal as a reference. The relation between RMBF determined by CM and RM was CM = 0.01 + 1.00.RM (r = 0.98, n = 1,080 data points) in the pigs, and CM = -0.19 + 0.92.RM (r = 0.97, n = 1,813 data points) in the dogs. CONCLUSIONS. Measurement of RMBF with CM yields values very similar to those of RM. Their use is less expensive and avoids all the disadvantages related to radioactivity, thus offering an alternative method for as many as five RMBF measurements in a single experiment.