Tokushima prefecture is the second largest producer of lotus roots in Japan, with an annual harvest of approximately 8,000 tons. In the present study, we determined the contents of amino acids in the flesh, joint, and peel of lotus roots of two cultivars, "Bicchu" and "Lotus", grown in Tokushima prefecture. Asparagine, glutamine, arginine and alanine accounted for more than 60％ of the total amino acids in the flesh of "Bicchu" and "Lotus" roots, while glutamine comprised around 5％ of the total amino acids in their joint and peel. When comparing the cultivars, "Lotus" roots contained the almost same level of γ-aminobutyric acid （GABA） than "Bicchu" roots, with a preferential distribution in the flesh. These results suggest the potential applications of the unused parts (joint and skin) of lotus roots grown in Tokushima prefecture as an ingredient in processed food products.