Objective: Retinoic acid (RA), the natural acidic derivative of vitamin A, can modulate the expression of specific genes and can induce some cell types, such as the mouse embryonic stem cells (mESCs), to differentiate in culture. mESCs treated with retinoic acid are induced to differentiate into neuron-like cells. One of the recently identified peroxisomal matrix proteins is peroxisomal protein (PeP). Previous studies have showed PeP in the adult mouse is mainly expressed in heart, skeletal muscle, and brain tissues. This expression pattern suggests a possible role for PeP in processes of neurogenesis. Therefore, the aim of this study was to assess the expression of PEP during neurogenesis. Materials and Methods: We performed a semiquantitative RT-PCR analysis to study of PEP mRNA expression in RA-treated and non-RA-treated in mouse embryonic stem cells (mESCs). Therefore mESCs cells were cultured for process of neurogenesis. The process of cell differentiation was chased and verified by immunostaining and gene expression of marker proteins for different stages of neurogenesis. Results: The data indicated that PEP mRNA expression level increased after 4 days treatment by RA significantly, while there was no increment in the level of PeP mRNA in untreated cells. Moreover, PeP gene expression was decreased in neural cells. Conclusion: This result indicated that the expression of PEP gene is inducible by retinoic acid treatment during the stage of neurogenesis. Thus further studies should be done to demonstrate the main function of PeP gene in this stage.