Sleep inertia refers to the transient physiological state of hypoarousal upon awakening, associated with various degrees of impaired neurobehavioral performance, confusion, a desire to return to sleep and often a negative emotional state. Scalp and intracranial electro-encephalography as well as functional imaging studies have provided evidence that the sleep inertia phenomenon is underpinned by an heterogenous cerebral state mixing local sleep and local wake patterns of activity, at the neuronal and network levels. Sleep inertia is modulated by homeostasis and circadian processes, sleep stage upon awakening, and individual factors; this translates into a huge variability in its intensity even under physiological conditions. In sleep disorders, especially in hypersomnolence disorders such as idiopathic hypersomnia, sleep inertia may be a daily, serious and long-lasting symptom leading to severe impairment. To date, few tools have been developed to assess sleep inertia in clinical practice. They include mainly questionnaires and behavioral tests such as the psychomotor vigilance task. Only one neurophysiological protocol has been evaluated in hypersomnia, the forced awakening test which is based on an event-related potentials paradigm upon awakening. This contrasts with the major functional consequences of sleep inertia and its potentially dangerous consequences in subjects required to perform safety-critical tasks soon after awakening. There is a great need to identify reproducible biomarkers correlated with sleep inertia-associated cognitive and behavioral impairment. These biomarkers will aim at better understanding and measuring sleep inertia in physiological and pathological conditions, as well as objectively evaluating wake-promoting treatments or non-pharmacological countermeasures to reduce this phenomenon.