Hairy roots induced from stems of Rubia cordifolia var. pratensis were cultured in the liquid medium under a variety of auxins to find the optimal condition for the growth and production of pigments. Culture of the hairy roots on NN liquid medium containing NAA 0.5 mg/l was best for growth of hairy roots. Production of yellow anthraquinone derivatives and purpurin in hairy roots was enhanced by the culture on NN liquid medium without auxins. Effects of L-phenylalanine, L-tyrosine and juglone, synthesized via the shikimic acid pathway, on growth and production of pigments in hairy roots were studied in the present study. Concentration of exogeneous L-phenylalanine. L-tyrosine and juglone in liquid culture system of hairy root containing NAA 0.1 mg/l was decreased quickly in its early stages of the culture period. Addition of juglone to NN liquid medium containing NAA 0.1 mg/l enhanced the productivity of pigments in hairy roots.