The free and protein-bound amino acid composition of the herb and roots of Smallanthus sonchifolius was analyzed by HPLC method. Fourteen free and fifteen protein-bound amino acids were determined in yacon herb, and three free and fourteen protein-bound amino acids in the roots. Among the free amino acids, proline (0.44 µg/mg) and aspartic acid (0.12 µg/mg) were dominant in the herb and proline (0.28 µg/mg) in the roots. Among the protein-bound amino acids, aspartic acid (18.58 µg/mg), glutamic acid (16.33 µg/mg) and proline (14.52 µg/mg) prevailed in the herb, and proline (3.14 μg/mg) in the roots. Fructose, sucrose and arabinose were identified in free form in the herb of S. sonchifolius applying gas chromatography-mass spectrometry (GC-MS). The polysaccharide complex was obtained from yacon herb, its yield was 5.13 ± 0.09%. Fructose (3.11 µg/mg) was the only monosaccharide identified in the hydrolysate of the obtained complex.