A phytochemical study was performed on the subterranean parts (roots and rhizomes) of Rubia peregrina. The substances were isolated from chloroform, ethyl acetate, and water soluble parts of the methanolic extract using several chromatographic techniques. 1-Hydroxy-2-methyl-9,10-anthraquinone (1), 1,3-dihydroxy-2-methyl-9,10-anthraquinone (2), and 1,3-dihydroxy-2-methoxymethyl-9,10-anthraquinone (3) were isolated from the chloroform phase; and asperuloside (4), asperulosidic acid (5), rubiadin 3-O-beta-primeveroside (6), lucidin 3-O-beta-primeveroside (7), deacetylasperulosidic acid (8), liriodendrin (9), and a new naphthoquinone glycoside, 2-hydroxy-3-O-beta-primeveroside naphthalene-1,4-dione (inkumoside, 10), from the aqueous phase. The structures of the compounds were elucidated by means of spectral analysis ((1)H-NMR, (13)C-NMR, (2)D-NMR-COSY, HMBC, HMQC-, EI-MS and ESI-MS).