We have previously isolated shikonin-producing and shikonin-nonproducing cell lines from the single cell cultures of Lithospermum erythrorhizon. In this study, in vitro translation products of poly(A)+ RNA isolated from these different cell lines were analyzed by two-dimensional polyacrylamide gel electrophoresis and visualized by autoradiography by labeling proteins with 35S-methionine. Comparison of translation products on 2-D SDS-PAGE showed the qualitative and quantitative changes in cell growth medium and pigment production medium. Especially, the shikonin-producing cell lines cultured on pigment-producing medium synthesized several new proteins. The result indicates that those proteins may be candidates for specific proteins related with shikonin production.