The GABAa receptor's structure is typical of most ligand-gated (ionotropic) receptors.  It is made up of five protein subunits arranged in a circle to form a pore, or channel, that remains closed until its specific ligand (in this case, GABA) binds to the recognition site. Each protein subunit is actually a string of amino acids which passes in and out of the cell membrane four times. At the extracellular end of this string is a large N-terminal; this end-chain is thought to mediate GABA-channel interactions. In the middle of the string is a large intracellular loop of amino acids with four sites where phosphorylation occurs.

Each of the five subunits that make up the receptor is about 50,000 daltons in size. These subunits have been labeled with Greek letters, such as alpha, beta, gamma and delta. It appears as though GABA requires both alpha and beta components in order to bind. GABAa receptors are typically made up of two alpha and two beta subunits among the five subunits, though the particular subunit composition often varies widely among brain regions and species. In fact, among GABAa receptors, 17 different combinations of subunits have been identified. Having a family of receptors that all share the same basic structure, but which differ in specific subunit composition, allows for a greater level of functional diversity. Each of the receptor varieties vary in binding affinity, channel activity, and the degree to which GABA binding is affected by different endogenous modulators. As a result, inhibitory signals can be more finely controlled. Such receptor heterogeneity also allows for more control at the genomic level, allowing post-synaptic cells to respond to changing developmental needs or variable activity at the synapse.