Abstract Upper airways (UA) are an organic component of the respiratory tract, they serve to respiration, respiratory tract protection and defense, phonation, deglutition, etc. The functions of UA are regulated by motor control of the oral, pharyngeal, and laryngeal muscles. UA typically stiffen and widen during inspiration mainly due to the activation of the alae nasi, genioglossus m., pharyngeal dilators, and laryngeal abductors. These and other UA muscles (e.g. laryngeal and pharyngeal constrictors) may express varoius activity patterns, actively shaping UA depending on species, arousal, respiratory drive, and behavior being executed. E.g. during coughing and sneezing laryngeal movement consists of abductions in inspiration and expiration and adductions in compression and subsequent constriction phase. The cricopharyngeus m., in cough expiration the superior pharyngeal constrictor and in the sneeze expiration the styloglossus and levator veli palatini m. are activated. Unlike in breathing or coughing, where UA serve to respiration-protection-defense, the pharyngeal phase of swallowing is essentially made by the coordinated action of a number of UA muscles. Motoneurons driving the UA muscles are located primarily in the hypoglossal and ambigual nuclei. Motor pattern of individual motoneuronal pools is determined by activation-inhibition-modulation from pre-motoneurons and other upstream neurons of the reflex circuits. Laryngeal and hypoglossal nerve activity is during breathing under command of respiratory central pattern generator. UA muscles are driven in inspiration primarily from augmenting, less from decrementing and constant inspiratory neurons. Number of additional inputs is involved in UA regulation during expirations and other motor behaviors. Anatomical and functional studies pointed out number of brainstem areas, such as the regions of solitary tract nucleus, hypoglossal ncl., trigeminal ncl., lateral tegmental field, raphé, the ventral and ventrolateral medulla, pontine parabrachial region, etc. with neurons related to UA motor control. Abundant connectivity of the neuronal network that controls UA patency employs almost all kind of receptors and neurotransmitter/neuromodulator systems. Among large number of diseases and disorders that relate to UA, primarily cholinergic, norepinephrine, and serotonergic tonic drives are implicated in those resulted from the reduced UA tone. Pharmacological and frequently simple surgical interventions may improve these conditions (snore, obturation) in patients. Recently, besides medicinal treatment, conditional procedures incorporating an exercise and practice, stimulation of appropriate afferent pathways, and combining reflex responses may offer promising therapies.