Modulation of GABA(A) receptor function and inhibitory synaptic transmission by phosphorylation has profound consequences for the control of synaptic plasticity and network excitability. We have established that activating alpha-calcium/calmodulin-dependent protein kinase II (alpha-CaMK-II) in cerebellar granule neurons differentially affects populations of IPSCs that correspond to GABA(A) receptors containing different subtypes of beta subunit. By using transgenic mice, we ascertained that alpha-CaMK-II increased IPSC amplitude but not the decay time by acting via beta2 subunit-containing GABA(A) receptors. In contrast, IPSC populations whose decay times were increased by alpha-CaMK-II were most likely mediated by beta3 subunit-containing receptors. Expressing alpha-CaMK-II with mutations that affected kinase function revealed that Ca(2+) and calmodulin binding is crucial for alpha-CaMK-II modulation of GABA(A) receptors, whereas kinase autophosphorylation is not. These findings have significant consequences for understanding the role of synaptic GABA(A) receptor heterogeneity within neurons and the precise regulation of inhibitory transmission by CaMK-II phosphorylation.