The effects of two light intensities on the concentration of several flavonoids were investigated in the cotyledons of common buckwheat seedlings. The study was performed on four days old seedlings of cvs. Hruszowska, Panda, Kora and Red Corolla. One group of seedlings was grown under exposure to 180 ± 20 μmol · m−2 · s−1 photosynthetically active radiation, whereas the other group was exposed to 360 ± 20 μmol · m−2 · s−1. The experiment lasted 5 days. The results revealed that light intensity induces changes in the levels of flavonols and flavones. Increased light intensity contributed to a decrease in the concentrations of all flavone C-glucosides: orientin (luteolin-8-C-glucoside) and iso-orientin (luteolin-6-C-glucoside), and apigenin: vitexin (apigenin-8-C-glucoside) and iso-vitexin (apigenin-6-C-glucoside). Simultaneously, a substantial increase in the content of flavonols, i.e. quercetin O-glycosides, was found. To the best of our knowledge, this is the first evidence to demonstrate the contrary responses of plant flavonols and flavones to light intensity. The content of anthocyanin also increased under exposure to higher light intensity. Our results indicate that quercetin O-glycosides can play a similar role to anthocyanins in the cotyledons of common buckwheat seedlings. Results of correlation analysis indicate that the increase in flavonol and anthocyanin concentrations in response to higher light intensity is maintained through reduced accumulation of flavones and proanthocyanidins.