Shikonin production was examined in a bubble column bioreactor system with the hairy roots of Lithosphermum erythrorhizon. The volumetric productivity was higher than those obtained from other reactor configurations with free or immobilized cells of the same cell line. The productivities of the bubble column reactor, with and without a product absorption trap, were 7.4 and 4.5 mg of shikonin/l/d, respectively. This indicated the importance of the product removal in the design and operation of the shikonin production system with hairy root culture.