The gamma-aminobutyric acidA/benzodiazepine receptor contains distinct ligand binding sites for hypnotic barbiturates and benzodiazepines. It is thought that barbiturate-induced sedation is produced, in part, by enhancing agonist binding to this receptor. The present study tested the hypothesis that pentobarbital would enhance benzodiazepine binding in a site-specific manner across the rat brain. In vitro receptor autoradiography was used to localize and quantitatively map [3H]flunitrazepam ([3H]FLU) binding in the absence and presence of pentobarbital in 133 brain areas. Each area demonstrated a statistically significant increase in [3H]FLU binding in the presence of in vitro pentobarbital (P < or = 0.05). Hindbrain nuclei dominated the top 20% of brain areas demonstrating the greatest pentobarbital-induced increases in [3H]FLU binding. The greatest mean percent increase in [3H]FLU binding occurred in the medulla, including areas known to be important for cardiovascular control, breathing, motor tone and regulating levels of arousal. These findings show that differential enhancement of benzodiazepine binding in the presence of pentobarbital occurred in brain areas controlling physiological functions known to be impaired by systemically administered pentobarbital.