Some Boraginaceous roots contain red colored pigments, alkannin and shikonin, which are used in therapy as well as in food and textile industry. For the quantitative analysis of these enantiomeric naphthaquinone derivatives, a cellolose carbamate based chiral column (Chiralcel OD) on HPLC was used by using hexane/2-propanol (90:10) as mobile system. The method was applied to determine the alkannin and shikonin contents of the roots of eighteen Boraginaceous plants and results were also compared with those of the LiChrospher RP-18 column.