cDNA microarray technique was used to study the mechanisms of liver injury caused by Huangyaozi at level of gene expression based on the biological functions of those differentially expressed genes. For the mice taking Huangyaozi for 15 days,there were 83 differentially expressed genes,among them 18 genes were up-regulated and 65 genes were downregulated, and the increase of serum ALT,AST and tissue total protein were notable. For the mice taking Huangyaozi for 30 days, there were 1658 differentially expressed genes,among them 917 genes were up-regulated and 741 genes were down-regulated. And the liver index, serum ALT and tissue total protein were all increased significantly but AST,AKP decreased significantly. There were 45 common differentially expressed genes in the two groups,among them 9 genes were upregulated,while the other 36 genes were down-regulated. According to the differentially expressed genes with different duration for taking Huangyaozi, the phased change about occurrence and development of liver injury was analyzed. The results indicated that the gene expression profile of mouse liver cell could be changed significantly by taking Huangyaozi, which might be important for elucidating the mechanisms of liver injury caused by Huangyaozi.