A new cyclodipeptide named as cordycedipeptide A, a new natural compound and two known compound were isolated from the culture liquid of Cordyceps sinensis (BERK.) SACC. Their structures were elucidated as 3-acetamino-6-isobutyl-2,5-dioxopiperazine (1), 3-isopropyl-6-isobutyl-2,5-dioxopiperazine (2) and 3,6-di(4-hydroxy)benzyl-2,5-dioxopiperazine (3) by 1D and 2D-NMR techniques. The cytotoxic assay showed compound 1 had the cytotoxic activities to L-929, A375, and Hela.