The present study explores an alternative method for antioxidants determination in buckwheat (Fagopyrum) samples. Buckwheat contains different amounts of the antioxidants rutin, quercetin and quercitrin in different plant parts. Buckwheat seeds are most commonly used as food; however, preparations from the herb can also be used as a rich source of rutin. Infrared spectroscopy was used for individual and sum quantification of rutin, quercetin and quercitrin in whole and ground flowers and leaves of seven different buckwheat species. Correlation coefficients R of calibration and independent validation set for rutin, quercetin and quercitrin were 1.00 and 0.98, 0.94 and 0.99, 0.99 and 0.95, respectively. Some of the developed models had accuracy comparable to the reference HPLC method. Additionally many different parameters that give an important insight into the FTIR technique are discussed (different plant parts, whole and ground untreated samples, 3 different resolutions, 7 spectra pre-treatments, using individual or averaged spectra, reducing spectral data input, considering additional non-spectral data). The implemented technique used no sample preparation, is non-destructive and uses very little amounts of sample. Result show that infrared spectroscopy can be a fast and environmentally friendly alternative technique for routine analysis of main flavonoids in aerial parts of buckwheat.