Introduction: Previously our laboratory identified a population of cells within the bone marrow, known as Beta2m-/Thy1+ bone marrow derived stem cells (BMSC) that are able to differentiate into hepatocytes. The effect of liver injury on the genes expressed by Beta2m-/Thy1+ BMSC is not known. The objective of this study was to determine the gene expression profile of Beta2m-/Thy1+ BMSC in common bile duct-ligated (CBDL) rats using DNA microarray analysis.Methods: Male Lewis rats underwent CBDL (n = 3)or a sham operation (n = 3). After 10 days, their bone marrow was harvested and Beta2m-/Thy1+ BMSC isolated using a two-step magnetic bead cell sorting technique. The mRNA expression profile of primary hepatocytes harvested from sham-operated male Lewis rats (n = 3) was used for comparison. The gene expression profile of Beta2m-/Thy1+ BMSC was determined using Affymetrix rat genemone U34a array.Results: In sham-operated rats, 24 common genes were found between Beta2m-/Thy1+ BMSC and normal hepatocytes. In the CBDL rats, 189 commonly expressed genes were found between the Beta2m-/Thy1+ BMSC and normal hepatocytes. Several liver-specific genes were identified including HNF1, Complement component C3, cholesterol esterase, Cytochrome P50 3A2, D site albumin promoter binding protein and mitochondrial import stimulation factor.Conclusions: Our results demonstrate that liver injury by CBDL alters the gene expression profile of Beta2m-/Thy1+ BMSCs. Cluster analysis of hepatocyte genes revealed Beta2m-/Thy1+ BMSCs from CBDL rats shared more genes in common with primary hepatocytes than Beta2m-/Thy1+ BMSCs from sham-operated rats.