A simple and reliable method for determination of quercetin glycosides and free quercetin in buckwheat flower, leaves, stems and achenes was developed. The method consists of flavonoid extraction from freeze-dried homogenous material in 50% v/v methanol solution and in presence of an antioxidant, cleaning of extract and analyte isolation using SPE. Analytical step uses capillary micellar electrokinetic chromatography. The working ranges, LOD and LOQ, recovery, precision and measurement uncertainty were calculated. The method is suitable for samples from buckwheat. The highest content of rutin was found in flowers of both kinds of buckwheat (99,400 mg/kg in F. esculentum, 108,000 mg/kg in F. tataricum). The free quercetin occurs in flowers and achenes of F. esculentum, whereas flowers and achenes of F. tataricum contained quercitrin.