This paper points out the usefulness of biopartitioning micellar chromatography (BMC) using capillary columns as a high-throughput primary screening tool providing key information about the oral absorption, skin permeability, and brain-blood distribution coefficients of 15 polyphenols (6 flavones, 2 flavonols, a flavanone, 2 flavan-3-ols, 3 phenolic acids, and a phloroglucinol) in a simple and economical way. For the compounds studied, except vicenin-2, rutin, chlorogenic acid, p-hydroxycinnamic acid, and 4-hydroxybenzoic acid, maximal oral absorption (>90%) can be expected, if there are not solubility problems or metabolic processes. On the other hand, the most retained compounds in BMC, that is, 5-hydroxyflavone, flavone, and flavanone, show the highest brain-blood distribution coefficients and skin permeability coefficients.