The severe hypomyelination seen in the CNS of untreated phenylketonuria (PKU) patients has been suggested to be the result of a defect in the process of myelination itself. Using chronic hyperphenylalaninemia (HPA) in rats as a model of PKU we have previously shown, by immunohistochemistry, that axonal maturation as well as myelination was severely retarded. In the present study we have used image analysis techniques to quantitate changes in myelin basic protein (MBP) and 200-kDa neurofilament protein (NF-H) immunostaining in the corpus callosum and cerebral cortical grey matter of HPA rats. No difference in the density of MBP+ myelin was observed in the corpus callosum after 24 days HPA treatment although the width of the tract was much reduced. In contrast there was a deficit in NF-H immunostaining. Large deficits in both myelin and axonal maturity were seen in the cortical grey matter. Following a 6-week recovery period, despite recovery in the corpus callosum, large deficits in both MBP and NF-H were still seen in all cortical layers. Deficits in NF-H immunostaining were two to three times greater than those for MBP. On increasing the recovery period to 18 weeks significant deficits in myelin remained in layers I-III of the cortical grey matter whereas NF-H immunostaining had returned to normal levels in all layers. Our data suggest a primary effect of HPA on neuronal development, in particular axonal maturation, with a secondary hypomyelination and show that permanent deficits in myelinated axons in outer cortical layers can result when myelination is severely inhibited during a critical developmental period.