Micellar electrokinetic capillary chromatography (MECC), using a phosphate buffer pH 7.0 and sodium dodecyl sulfate as the surfactant, was found suitable for the separation of structurally similar flavan-3-ols and related dimeric proanthocyanidins. A total of 20 substances has been tested, 17 of which were successfully separated simultaneously in less than 7 minutes. Retention of the investigated compounds by the SDS micelles is affected by (i) the stereochemistry of the heterocycle of the flavan-3-ol skeleton, (ii) the molecular size, the number and position of free phenolic hydroxy groups, and (iii) the type of acyl residues attached at the C-3 hydroxy function. The method was successfully applied to the phytochemical analysis of tannin enriched extracts of Cistus incanus L. ssp. incanus and C. salvifolius L. (Cistaceae), two traditionally used medicinal plants.