Objective: The PPARs (peroxisome proliferator-activated receptors) are members of the nuclear hormone receptor superfamily. Three major isoforms of PPARs (α, β and γ) have been identified that each with a possibility of different ligands, target genes and biological roles. The expression of PPARα, β and γ varies widely from tissue-to-tissue. PPAR γ has been demonstrated to play an important role in the regulation of cell differentiation. PPAR γ has 2 isoforms termed: γ1, γ2, which are arisen by differential transcription start sites and alternative splicing. In order to see the importance of PPAR γ1 in differentiation process of embryonic stem cells, the present study was undertaken. Materials and Methods: Endodermal differentiation of mESCs (Royan B1 cell lines) cells was induced by culturing the cells in N2B27 media including for 5 days under treatment by Activin A at final concentration of 100 ng/ml with daily medium change. Treatment pursued by the same condition supplemented with retinoic acid (RA) (0.1 µM) in place of Activin A for more three days. In order to chase the mRNA level of PPAR γ1, Total RNA was extracted from mESC, cells before RA treatment (d5) and after reaching to the endodermal cell fate (d8, DE) and cDNA synthesis was carried out to perform a real time quantification analysis for PPAR γ1. Results: Despite a decrease in expression pattern of PPARγ1 in d5 cells, the results revealed an increasing expression pattern of PPARγ1 in DE differentiated cells (d8, DE) relative to mESC and d5, which was significant at p < 0.05. Conclusion: In the present research, we have attempted to have a further look into the expression level of PPAR γ1 gene during the differentiation of stem cells to definitive endoderm. In conclusion, our data clearly indicated that an increment in PPAR γ1 upon RA treatment may be somehow is involved in regulation of stem cells differentiation in to definitive endoderm which could be clarified in further studies.