The determination of the sum of flavonoid compounds in extracts from inflorescences (expressed as mgL(-1) of apigenin) and leaves (expressed as mgL(-1) of linarin) of Cirsium oleraceum and Cirsium rivulare species by flow injection system with chemiluminescence detection (FI-CL) has been carried out. The method is based on the strong enhancement by polyphenols occurring in both plants of the CL signal generated by the reaction of cerium(IV) with rhodamine 6G in a sulfuric acid medium. Under the optimized conditions, the linear working ranges of 0.1-10 and 2.5-50μmolL(-1) were obtained for apigenin and linarin, respectively. The developed method is simple, sensitive with the detection limits of 38nmolL(-1) (apigenin) and 840nmolL(-1) (linarin) and offers high sample throughput (up to 300 samples per hour). The relative standard deviation was 0.62% and 3.75% for 10 measurements of 5μmolL(-1) apigenin and linarin, respectively. The proposed method has been successfully applied to determine the flavonoids/antioxidant levels in aqueous and methanolic extracts from inflorescences and leaves of C. oleraceum and C. rivulare. A possible mechanism of the enhancement of cerium(IV)-rhodamine 6G CL system by polyphenols was briefly discussed. For comparative studies, the antioxidant activity of C. oleraceum and C. rivulare extracts was also evaluated by spectrophotometric 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radical scavenging method.