The expression of mRNAs for the GABAA receptor subunits alpha1, alpha6, beta2, beta3, gamma2 and delta in single mouse cerebellar granule cells and cortical interneurons were analysed by RT-PCR and correlated to their midazolam and zinc modulation of agonist-induced receptor currents. The registration of molecular and electrophysiological data from each cell allowed us to estimate the significance of individual subunits and their two-factor interaction for modulation. The presence of alpha6 decreased midazolam modulation, but statistical analysis also suggested interactions of alpha6 with beta3 and gamma2 with respect to midazolam modulation. Zinc modulation was decreased by the presence of gamma2, and analysis points to an beta3 effect as well as an interaction between gamma2 and delta in zinc modulation. Thus, our model confirmed, in single native cells, the known effects of alpha6 in midazolam and gamma2 in zinc modulation, and additionally pointed to significant subunit interactions that need to be further tested in recombinant receptors. The present study offers a method to identify subunit interactions in heteromeric receptor complexes.