Recent advances in the derivation of functional cells from pluripotent stem cells have raised hope for cell therapy to treat liver ailments. They have enhanced the prospects of developing reliable in vitro models for liver diseases and drug toxicity screening. A differentiation protocol mimicking key signaling cues of embryonic development was developed to direct stem cells (ES) towards the hepatic fate and express key hepatic markers and functions. While these results are encouraging, most directed differentiations from stem cells to the target cell types are hampered by lack of functional maturity, cell heterogeneity and low cell yields limiting their translation to the clinic. These cells are therefore refereed to hepatocyte-like cells (HLCs). An integrative strategy was employed including both experimental techniques as well as a systems-based analysis towards enhancing the product quality and yields of HLCs. Functional maturity was enhanced by initiating three dimensional spheroid formation upon differentiation. Enrichment of hepatic cells using selective medium conditions was performed to obtain higher fraction of cells with the desired properties. Cell expansion was incorporated during differentiation to improve cell yields. Several additional strategies have been used to increase hepatocyte maturity in literature including co-culture and transfection with transcription factors. These methods including ours have shown improvement, however a universal gap to maturation is still present when compared to primary hepatocytes. Comparison of transcriptome data of differentiation to embryonic liver development can elucidate the genetic roadblocks preventing ES cells from reaching the functional maturity of their tissue counterparts. Transcriptome data was compiled from various depositories for mouse fetal liver development (from E8.5 to post-natal). Transcriptome data was obtained during the time course of our human hepatic differentiation protocol and was augmented with human in vitro hepatic differentiation data in the public depository. Interestingly, majority of the HLCs are similar irrespective of the cell source and protocol. The entire cohort of HLCs clustered separately from the primary hepatocytes and adult liver indicating an inherent roadblock to maturation. The transcriptome data of human ES hepatic differentiations was then integrated with mouse liver development using a unique approach. This allowed us to identify the corresponding development stage at which the in vitro stem cell differentiation is blocked. The analysis uncovered a pivotal gene set with contrasting profiles in ES differentiation and mouse liver development that merit combinatorial genetic intervention to enhance maturation of ES derived hepatocytes. Thus, one can envision the availability of stem cell based liver therapies in the not so distant future.