Phenylketonuria (PKU) is an inborn error of amino acid metabolism. Phenylalanine hydroxylase (PAH) mutations resulting reduced enzyme levels lead to accumulation of phenylalanine (Phe) in brain, if Phe diet is not restricted. Patients with PKU show neurophysiological abnormalities including demyelination and cognitive defect. How PAH defect causes events seen in PKU is not obvious. Therefore, expression analysis was performed in the brain of a mouse model for PKU. Microarray expression profile of the brain showed lower expression of myocilin (Myoc) in the PKU mouse. Reduced expression of Myoc was further confirmed by one-step real-time RT-PCR. Western blotting analysis of the brain using equal quantities of protein showed a thin band in PKU compared to a prominent band in the wild type brain. In addition, expression of genes associated with transcription was found to be altered in the PKU mouse brain as observed by microarray analysis. These data suggest that PAH defect alters other genes expression likely to contribute neurophysiological abnormalities seen in the mouse, if documented also in patients with PKU.