More than 30 genetics factors required for peroxisome biogenesis are identified so far. The formation and growth and proliferation of peroxisomes are completely dependent to proper functions of these factors. Several homologs of these factors have been cloned and characterized in mammals and human. Any pathophysiological functions in embryonic stages of such genetics factors cause formation of human peroxisome disorders like Zellweger syndrome as complementation group 12 of this disorder is caused by dysfunction of PEX3. One of the symptoms of these disorders is improper development of nervous system due to impairment in reduction of oxidative components by peroxisomes and plasmalogen synthesis which is one of the major constituents in membranes. Due to lack of intensive studies related to involvement of Peroxisomal biogenesis factors and neural differentiations, the aim of the present study is unraveling this mechanism. In this research we aimed to clone PEP cDNA and study the intracellular location of this protein and assess the expression level of its mRNA during neural differentiation besides of its interaction with binding partners.