Objective: Peroxisomal matrix protein is mainly expressed in heart, skeletal muscle, and brain tissues. To study the expression of peroxisomal protein (PEP) during neurogenesis, we here employed P19 cells as an in vitro model of neural differentiation.Materials and Methods: Expression pattern of PEP was investigated under distinct steps of differentiation by real time PCR. Time course study of the PEP expression revealed that expression increased prominently during aggregate formation in P19 cells. The expression level of endogenous genes such as MAP-2, PEP, catalase and PEX3 as peroxisomal markers, compared withβ-tubulin as housekeeping gene were monitored during different stages of neural differentiation.Results: The results were semi-quantified and revealed the highest relative expression of PEP in cell aggregates when treated by RA. In contrast, in the absence of RA, the relative expression of PEP was at the lowest level in aggregates and gradually increased in later stages. Unlike expression of PEP and MAP2 which are stage specific dependent, the expression levels of the other two peroxisomal markers, catalase and PEX3, were not stage dependent.Conclusion: The results of this study showed that elevated level of PEP expression was dependent on RA. A further insight in PEP gene expression, quantitative real time PCR results showed significant difference in PEP expression in presence and absence of RA.