Propolis is a resinous hive product rich in antioxidant compounds. Capillary electrophoresis coupled to mass spectrometric detection can provide selective information about the analytes present in complex extracts of propolis and has turned out to be an attractive alternative to HPLC methods. Therefore, a CE-ESI-MS method has been developed for the analysis of antioxidant compounds obtained from propolis. For this purpose, different electrophoretic parameters such as the nature, pH, and concentration of the separation buffer, as well as electrospray parameters (dry gas temperature and flow, nebulising gas pressure, and make-up flow) have been carefully optimised. Different phenolic compounds (e.g. pinobanksin 3-acetate, naringenin, pinocembrin, chrysin, daidzein, quercetin 3',7-dimethyl ether, apigenin, and kaempferid) could be detected. To confirm the identity of the phenolic compounds in propolis extracts, accurate mass data of the molecular ions were obtained by TOF MS. Limits of detection ranging from 6 mg/100 g of raw propolis for chrysin to 58 mg/ 100 g of raw propolis for luteolin, were obtained.