The Coomassie brilliant blue protein assay is commonly used because of its sensitivity and convenience, but it is not well understood on a molecular level. This study attempts to gain better understanding of the assay system through spectrophotometric binding studies carried out on selected proteins under solvent conditions characteristic of the normal protein assay. The studies were generally conducted at high protein/dye concentration ratios, where only the high-affinity dye binding sites would be occupied. Modified Scatchard and Hill analyses show that these high-affinity sites are few in number compared to the total number of dye-binding sites on a given protein. The magnitudes of the high-affinity binding constants are typical of noncovalent binding interactions.