The simple extraction of flours samples followed by free amino acids determination procedures was studied and optimised. The conditions of amino acids derivatisation reaction with ninhydrin for chromatographic determination of free amino acids sum was discussed. The developed method was processed in terms of linearity, precision, accuracy, and limits of detection and quantification. Moreover, capillary isotachophoresis and HPLC methods were applied for individual free amino acids determination. The proposed extraction procedure is simple, fast and convenient for different flours samples. Studied procedures were used for free amino acids determination in twelve gluten-free flour samples (corn, oat, soy, rice, pumpkin, millet, peanut, hemp seed, buckwheat, amaranth, pea and chickpea) and the obtained results were compared with wheat flour.