The methanolic extract of the roots of Lithospermum erythrorhizon (Boraginaceae) was found to show inhibitory activity towards farnesyl protein transferase (FPTase). Bioassay-guided fractionation of the methanolic extract resulted in the isolation of three naphthoquinone compounds, as inhibitors of FPTase. These compounds inhibited the FPTase activity in a dose-dependent manner.