To probe further the contributions of cholinergic rostral pontine systems in control of breathing, we designed this study to test the hypothesis that microdialysis (MD) of the muscarinic receptor antagonist atropine into the pontine respiratory group (PRG) would decrease breathing more in animals while awake than while in NREM sleep. In 16 goats, cannulas were bilaterally implanted into rostral pontine tegmental nuclei (n ϭ 3), the lateral (n ϭ 3) or medial (n ϭ 4) parabrachial nuclei, or the Kölliker-Fuse nucleus (KFN; n ϭ 6). After Ͼ2 wk of recovery from surgery, the goats were studied during a 45-min period of MD with mock cerebrospinal fluid (mCSF), followed by at least 30 min of recovery and a second 45-min period of MD with atropine. Unilateral and bilateral MD studies were completed during the day and at night. MD of atropine into the KFN at night decreased pulmonary ventilation and breathing frequency and increased inspiratory and expiratory time by 12-14% during both wakefulness and NREM sleep. However, during daytime studies, MD of atropine into the KFN had no effect on these variables. Unilateral and bilateral nighttime MD of atropine into the KFN increased levels of NREM sleep by 63 and 365%, respectively. MD during the day or at night into the other three pontine sites had minimal effects on any variable studied. Finally, compared with MD of mCSF, bilateral MD of atropine decreased levels of acetylcholine and choline in the effluent dialysis fluid. Our data support the concept that the KFN is a significant contributor to cholinergically modulated control of breathing and sleep.non-rapid eye movement sleep; pons FOR MANY YEARS, ACETYLCHOLINE (ACh) has been known to play a role in the control of breathing (14) and sleep (3). In the medial pontine reticular formation (mPRF), endogenous ACh release causes state-dependent changes in respiratory control (2) and can stimulate rapid eye movement (REM) sleep (22). Microadministration of the cholinergic agonists carbachol (mixed cholinergic agonist), bethanechol (muscarinic agonist), and neostigmine (acetylcholine esterase inhibitor) into the mPRF are all known to generate this effect (1,2,18,22,27), whereas the muscarinic antagonist atropine can block this effect (1). Indeed, mPRF cholinoceptive mechanisms can cause state-dependent changes in the firing rates of respiratory neurons in the parabrachial nuclei (16). These studies provide evidence of anatomic connectivity from the mPRF to the pontine respiratory group (PRG). Evidence of projections in the reverse direction, from the PRG to the mPRF, is provided by microinjection of fluorescent dyes into the PRG, resulting in ipsi-and contralateral positive regions in the mPRF as well as in the dorsal respiratory group and ventral respiratory group in the medulla (20). However, studies of the connectivity between brain stem respiratory neurons performed using chronically implanted arrays of microelectrodes emphasized "a sparse distribution of functional connections," which suggests that interactions between brai...