The GABAA receptor is the main inhibitory receptor in the brain and its subunits originate from different genes or gene families (α1-α6, β1-β3, γ1-γ3, δ, ε, θ, π, or ρ1-3). In the mouse brain the anatomical distribution of GABAA receptor subunit mRNAs so far investigated is restricted to subunits forming benzodiazepine-sensitive receptor complexes (α1-α3, α5, β2, β3 and γ2) in the forebrain and midbrain as assessed by in situ hybridization (ISH). In the present study the anatomical distribution of the GABAA receptor subunits α1-α6, β1-β3, γ1-γ2 and δ was analyzed in the mouse brain (excluding brain stem) by ISH and immunohistochemistry (IHC). In several brain areas such as hippocampus, cerebellum, bulbus olfactorius and habenula we observed that mRNA levels did not reflect protein levels, indicating that the protein is located far distantly from the cell body. We also compared the distribution of these 12 subunit mRNAs and proteins with that reported in the rat brain. Although in general there is a considerable correspondence in the distribution between mouse and rat brains, several species-specific differences were observed.