mRNA for GABAAR subunits and synaptophysin is differentially regulated in cortex and medulla across the circannual cycle. Quantitative analysis of mRNA for GABAAR subunits ε, δ, and α1–4 and synaptophysin in the medulla and cortex of the 13-lined ground squirrel during summer active (SA), torpor (T), and interbout arousal (IBA). In the medulla, GABAA ε-mRNA was >3.5-fold greater in T than SA, whereas cortical mRNA did not change. During IBA, medullary GABAAR δ mRNA was 20% of SA. Cortical δ-subunit mRNA did not change with behavioral state. GABAAR α-subunit mRNA changed with behavioral state only in cortex. Synaptophysin mRNA changed in cortical but not medullary samples. Data are normalized to SA. *P < 0.05, different from SA. #P < 0.05, different from IBA. Error bars indicate SE.