In a continuing program to discover new anticancer agents from plants, especially naphthoquinones from the Alkanna genus, Alkanna cappadocica was investigated. Bioassay-guided fractionation of a dichloromethane/methanol (1:1) extract of the roots led to the isolation of four new and four known naphthoquinones. The known compounds are 11-deoxyalkannin (1), beta,beta-dimethylacrylalkannin (2), 11-O-acetylalkannin (3), and alkannin (4). The new compounds 5-O-methyl-11-deoxyalkannin (5), 8-O-methyl-11-deoxyalkannin (6), 5-O-methyl-11-O-acetylalkannin (7), and 5-O-methyl-beta,beta-dimethylacrylalkannin (8) were characterized by spectroscopic analyses (LC-ESIMS, 1D and 2D NMR). Cytotoxicity of the isolated compounds was evaluated versus 12 human cancer cell lines, HT-29, MDA-MB-231, PC-3, AU565, Hep G2, LNCaP, MCF7, HeLa, SK-BR-3, DU 145, Saos-2, and Hep 3B together with two normal cell lines, VERO and 3T3, by using the MIT assay. Compound 7 showed remarkable cytotoxicity with IC50 values between 0.09 and 14.07 mu M. It was more potent than the other compounds in six out of 12 cancer cell lines and the positive controls doxorubicin and etoposide. The mono-O-methylated alkannin derivatives and their cytotoxicities are reported for the first time.