Alpha-synuclein is an evolutionary highly conserved neuronal protein localized in presynaptic nerve terminals. The protein has been suggested to be involved in the pathogenesis of neurodegenerative diseases, but little is known about the physiological function of the protein. In the present study we used newborn, three, 14, 93 and 710-day-old rats to examine the expression of alpha-synuclein messenger RNA and protein during development of the hippocampus and cerebral cortex. Using in situ hybridization and an S1 nuclease protection assay, we found a high expression of alpha-synuclein messenger RNA during early postnatal development, followed by a marked decrease between postnatal days 14 and 93. In contrast, the amount of alpha-synuclein protein, as determined by immunoblotting, continued to increase throughout development and remained at a high level for at least two years. The persistent high expression of alpha-synuclein protein throughout development suggests that the protein is involved in maintaining synaptic function. Furthermore, the discrepancy between the levels of alpha-synuclein messenger RNA and protein after postnatal day 14 indicates that the amount of alpha-synuclein is determined by post-transcriptional regulation, and not by messenger RNA expression alone. To estimate the changes of alpha-synuclein expression per synapse, we compared the developmental expression of alpha-synuclein with synaptophysin, a well-established synaptic marker. The alpha-synuclein/synaptophysin messenger RNA and protein ratio was high during early development, but low in adult (postnatal day 93) and old (postnatal day 710) rats. This could indicate a higher expression of alpha-synuclein per synapse during early development.