Objective To study the function of liver stem cells during at liver regeneration(LR) at transcriptional level. Methods The liver stem cell growthand differentiationrelated genes were obtained by data collection and literature review, and the gene expressions in rat regenerating liver were checked by Rat Genome 230 2.0 array. The relativity of the LRassociated genes was identified by comparing the discrepancy of gene expression changes between partial hepatectomy (PH) group and sham operation (SO) group. Results Fifty genes were found to be related with liver regeneration. The initial and total expressing gene numbers occurring in the initiation phase of liver regeneration (0.5-4 hours after PH), GSUB>0/SUB>/GSUB>1/SUB> transition (4-6 hours after PH), cell proliferation (6-66 hours after PH), cell differentiation and structure function reconstruction (72-168 hours after PH) were 24, 10, 21, 2 and 24, 23, 46, 26 respectively, indicating that the related genes were mainly triggered during the initiation phase, and worked at different phases. The total frequencies of their up- and down-regulation expression were 153 and 123 respectively, demonstrating that the expression of the major genes increased, and the minority decreased. Their expression profiles were classified into 6 types, indicating that the activities mentioned above were diverse and complicated during liver regeneration. Conclusion The growth and differentiation of liver stem cells are enhanced during liver r