The relationship between the NMDA receptor NR1 subunit mRNA and the binding of the NMDA channel ligand [3H]MK-801 was studied during the late embryonic and early postnatal period in various regions of the rat CNS. NR1 mRNA was detectable at embryonic day 18 in all regions analysed and specific binding sites for [3H]MK-801 were present in the cerebral cortex at least from the day of birth, with an unaltered affinity up to postnatal day 15. In the cortex, hippocampus and hypothalamus there was a pronounced increase in binding between postnatal day 8 and 15, while the NR1 mRNA levels during this period were unchanged or even decreased. A more parallel developmental profile of mRNA content and binding levels were seen in the medulla and spinal cord. In the cerebellum the profile was different compared to the other regions, with a clear increase in NR1 mRNA between postnatal day 8 and 15 without any change in the [3H]MK-801 binding level. We conclude that even though the NR1 subunit alone possesses all the properties characteristic for the NMDA receptor, we cannot find a clear relationship between the level of its mRNA and the amount of [3H]MK-801 binding in the developing rat CNS.