We have compared the expression pattern of NMDA receptor subunits (NR1 and NR2A-D) and NR1 splice variants (NR1-1a/1b,-2a/2b,-3a/3b,-4a/4b) in motor neuron populations from adult Wistar rats that are vulnerable (hypoglossal, XII) or resistant (oculomotor, III) to death in amyotrophic lateral sclerosis (ALS). The major finding was higher levels of expression of the NR2B subunit in the hypoglossal nucleus. Quantitative real-time PCR showed that NR1 was expressed at a greater level than any of the NR2 subunits (>15 fold greater, P<or=0.05, n = 11 animals), while conventional RT-PCR showed no difference in NR1 splice variant expression (with all variants except NR1-3 detected in both nuclei; n = 6 animals). Within III, the NR2B subunit was expressed 1.7 to 2.6-fold lower than the other NR2 subunits (P<or=0.05), while in XII all NR2 subunits were expressed at equal levels. When comparing levels between the 2 nuclei, mRNA for the NR2B subunit was expressed 2.1-fold higher in XII compared to III (P<or=0.05), while their was no difference in mRNA expression for the other subunits. Immunohistochemical analysis confirmed greater NR2B protein levels within individual hypoglossal neurons compared to oculomotor neurons (1.8-fold greater, P<or=0.05, n = 5 animals). Lower expression of the NMDA NR2B subunit may constitute one factor conferring protection to oculomotor neurons in ALS.