1. The glycine receptor (GlyR) alpha2A and alpha2B splice variants differ by a dual, adjacent amino acid substitution from alpha2A(V58,T59) to alpha2B(I58,A59) in the N-terminal extracellular domain. 2. Comparing the effects of the GlyR agonists, glycine, beta-alanine and taurine, on the GlyR alpha2 isoforms, revealed a significant increase in potency for all three agonists at the alpha2B variant. 3. The sensitivities of the splice variants to the competitive antagonist, strychnine, and to the biphasic modulator Zn(2+), were comparable. In contrast, the allosteric inhibitor picrotoxin was more potent on GlyR alpha2A compared to GlyR alpha2B receptors. 4. Coexpression of alpha2A or alpha2B subunits with the GlyR beta subunit revealed that the higher agonist potencies observed with the alpha2B homomer were retained for the alpha2Bbeta heteromer. 5. The identical sensitivity to strychnine combined with a reduction in the maximum current induced by the partial agonist taurine at the GlyR alpha2A homomer, suggested that the changed sensitivity to agonists is in accordance with a modulation of agonist efficacy rather than agonist affinity. 6. An effect on agonist efficacy was also supported by using a structural model of the GlyR, localising the region of splice variation to the proposed docking region between GlyR loop 2 and the TM2-3 loop, an area associated with channel activation. 7. The existence of a spasmodic mouse phenotype linked to a GlyR alpha1(A52S) mutation, the equivalent position to the source of the alpha2 splice variation, raises the possibility that the GlyR alpha2 splice variants may be responsible for distinct roles in neuronal function.