To explore the molecular basis of inducible differentiation of embryonic stem cells into hepatocyte-like cells, a proteomic strategy was utilized to examine the global protein expression alterations after early-stage differentiation of a mouse D3 embryonic stem (ES) cell line along hepatic lineage. The undifferentiated D3 cells were treated stepwise with combinations of defined chemicals and growth factors. The differentiated cells were identified by hepatocyte-like morphology, expressed liver-specific markers as well as the evidence of glycogen storage. The subsequent proteomic separation and identification were performed with 2-DE followed by MALDI-TOF-MS/MS analysis. Of the 119 differentially displayed protein spots analyzed, 90 spots presenting 64 distinct proteins were finally identified. The interested protein expressions were validated by Western blotting such as albumin and cytokeratin-8. Bioinformatic annotations indicated that this set of proteins was enriched with transcription, translation regulation and protein processing, energy/metabolism and chaperone functions. A part of them had been found to be involved in the differentiation of mouse ES cells. Interestingly, approximately 40% of these proteins had been previously reported as being dysregulated in hepatocellular carcinoma. It suggested that these changed proteins may be candidate regulators of ES cell differentiation, some of them may be specific to hepatic differentiation.