Inhibition in the central nervous system is largely mediated by local-circuit neurons that release GABA (gamma-amino-butyric acid). GABAA-receptors play a major role in virtually all brain physiological functions and serve as targets for numerous classes of drugs, used both in clinical practice and as research tools. These receptors are heteropentamers, alpha1 being the most widely occurring subunit; therefore it is the best candidate to be studied in pathological conditions where the inhibitory system might be altered (e.g. epilepsy). We compared quantitatively the regional distribution of GABAA-receptor alpha1-subunit (GABAAR-alpha1) expression in three brain areas: neocortex, hippocampus and cerebellum by RT-qPCR. TaqMan probe was used in order to avoid detection of non-specific amplification products and synaptophysin as internal control. This substance was chosen because it has a stable expression restricted to neurons, and contrary to GAPDH, the most commonly used reference gene for expression analysis, synaptophysin expression is not modified in animal models of epilepsy. Expression of synaptophysin was higher than expression of GABAAR-alpha1 in all samples from the central nervous system. The latter was significantly different among the studied brain areas. It was the smallest in the hippocampus, intermediate in the neocortex and the highest in the cerebellum. Interanimal differences were small for any brain region under study. These results indicate that combination of TaqMan real-time PCR method with synaptophysin as internal control can reliably measure the relative expression of GABAAR-alpha1 mRNA, and are suitable for investigating the modifications that appear under pathological conditions and/or diverse experimental paradigms.