Previous studies have shown that bone marrow beta 2m(-)/Thy-1+ hepatic stem cells (BMHSCs) were able to engraft in vivo and differentiate into functioning hepatocytes in vitro. Our transcriptomic profiling on BMHSCs derived from rats subjected to common bile duct ligation (CBDL) demonstrated CBDL-derived beta 2m(-)/Thy-1+ BMHSCs expressed hepatocyte-like genes and shared more commonly expressed genes with hepatocytes, suggesting that an "on-site" priming of BMHSCs into hepatocyte lineage was initiated under the condition of CBDL. In this paper, transcriptomic profiling was carried out on livers from rats with CBDL to identify candidate factors released from cholestatic livers possibly involved in the priming of BMHSCs using Affymetrix Rat Genome U34A arrays. In CBDL rat livers, 1,091 probe sets were differentially expressed, of which 188 up-regulated probe sets were annotated as "extracellular" components. Gene ontology analysis showed many up-regulated genes belonged to cytokines, chemokines and growth factors, including Il1b, Il18, Ptn, Spp1, Grn, Ccl2, Cxcl1, Pf4, Tgfb, and Tgfb3. Cell differentiation and proliferation regulation factors such as Dmbt1, Efna1, Lgals1, Lep, Pmp2, and Gas6 were also induced in CBDL livers. Furthermore, many proteolysis and peptidolysis genes such as Mmp2, Mmp12, Mmp14, and Mmp23 were up-regulated in CBDL livers. Gene expression profiling showed that many cytokine-, chemokine-, growth factor- as well as certain extracellular protein-related genes were induced in CBDL livers, suggesting that these genes may be involved in hepatic BMHSCs priming.