In this study, we attempted to determine the anti-inflammatory activity of a medicinal plant huang-lian using gene expression profiles as an index. Huang-line extracts (CEXs) were prepared from seven different plant origins and compared for their chemical composition and biological activity. In order to achieve this, RAW264.7 cells were treated with CEXs in the absence or presence of LPS for 6 h, and the differential gene expression profiles were analyzed using oligonucleotide microarrays. The alkaloid content of CEXs was determined by high performance liquid chromatography analysis. Evaluation of anti-inflammatory activity of CEXs was by measuring a decrease in cytokines and nitric oxide production in LPS-stimulated RAW264.7 cells. Hierarchical clustering analysis revealed that three CEXs from Coptis chinensis formed a cluster separate from the other four CEXs in LPS-stimulated cells, and were the most effective anti-inflammatoryagents. The extract prepared from Picrorrhiza kurrooa neither induced any changes in gene expression profiles nor possessed any anti-inflammatory activity. The extract from Jeffersonia dubia, which exhibited the highest cytotoxicity among the CEXs tested, was most effective in suppressing LPS-induced nitric oxide production but was not able to inhibit proinflammatory cytokine production. The results obtained in this study demonstrate that overall gene expression profiles of the extracts correlated well with their biological activity and that CEXs prepared from plants of diverse origins vary in their biological activity. These data also suggest that gene expression profiles may serve as a good indicator for the pharmacological activities of medicinal plants arising from diverse origins.