Antibodies against glutamic acid decarboxylase (GAD-Abs) are associated with cerebellar ataxia, which is refractory to treatment with GABAergic drugs. To investigate the GABAergic neuronal system in vivo, we performed a combined positron emission tomography (PET) study with [(11)C]-flumazenil and [(18)F]-fluorodeoxyglucose (FDG) in three patients with cerebellar ataxia with GAD-Abs. The GABA-A receptor function was investigated using flumazenil, which is a selective GABA-A receptor ligand, while FDG-PET using a three-dimensional stereotactic surface projection analysis was performed to estimate the metabolic rates of glucose (MRGlc) in the patients. GABAergic drugs showed no efficacy for the cerebellar ataxia in all three patients, and all three displayed a significant decrease in flumazenil binding in the cerebellum. No MRGlc decrease in the cerebellum was found in the two patients who presented with amelioration of cerebellar ataxia following intravenous immunoglobulin (IVIG) therapy, whereas a significant MRGlc decrease in the cerebellar hemisphere was observed in another patient who showed severe cerebellar atrophy on magnetic resonance images and no response to the IVIG therapy. The decreased flumazenil binding in the present patients indicated cerebellar GABA-A receptor impairment, which may be due to either neuronal cell loss, as demonstrated by the decreased MRGlc, or a dysfunction in GABAergic neuronal inhibition. Although GAD-Abs have been postulated to prevent the synthesis of GABA, resulting in decreased GABAergic transmission, the GABA-A receptor impairment may play another pathogenic role in cerebellar ataxia associated with GAD-Abs resulting in a condition refractory to GABAergic drug therapy.