The simultaneous determination of twelve different flavonoids, pinocembrin, acacetin, chrysin, rutin, catechin, naringenin, galangin, luteolin, kaempferol, apigenin, myricetin, and quercetin, two phenolic acids, cinnamic acid and caffeic acid, and one stilbene derivative, resveratrol, in propolis extracts used in medicine has been investigated by capillary zone electrophoresis (CZE). With a buffer constituted by sodium tetraborate 30 mm, pH 9.0, and 15 kV applied voltage, the 15 polyphenols were separated on an uncoated fused-silica capillary within 40 min using normal polarity. Under the experimental conditions used, a linear relationship was calculated between the CZE migration times and the molecular weight of polyphenols' expression of the increasing amount of their hydroxyl groups and polarity. Regression equations revealed a linear relationship (correlation coefficients > 0.97) between the peak area of each polyphenol species and their concentration, from 6 to 120 ng. The levels of analytes in three different propolis extracts, ethanolic, aqueous-ethanolic and aqueous-glycolic, used to prepare various commercial medicinal products, were determined. The aqueous-ethanolic propolis extract showed a great percentage of caffeic acid, galangin, quercetin, and chrysin, whilst the ethanolic preparation was composed of a great amount of resveratrol, chrysin, and caffeic acid. On the contrary, the aqueous-glycolic propolis preparation was composed of approx. 11 % of caffeic acid and a low amount of the other identified flavonoids due to the presence of approx. 85% of nonidentified compounds. CZE represents a valuable method for the qualitative and quantitative assay of the most relevant polyphenol components of propolis, representing an alternative to obtain typical fingerprints of propolis and a reliable identification of a large number of propolis polyphenolic species.