It is traditionally believed that cerebral activation (the presence of low voltage fast electrical activity in the neocortex and rhythmical slow activity in the hippocampus) is correlated with arousal, while deactivation (the presence of large amplitude irregular slow waves or spindles in both the neocortex and the hippocampus) is correlated with sleep or coma. However, since there are many exceptions, these generalizations have only limited validity. Activated patterns occur in normal sleep (active or paradoxical sleep) and during states of anesthesia and coma. Deactivated patterns occur, at times, during normal waking, or during behavior in awake animals treated with atropinic drugs. Also, the fact that patterns characteristic of sleep, arousal, and waking behavior continue in decorticate animals indicates that reticulo-cortical mechanisms are not essential for these aspects of behavior.

These puzzles have been largely resolved by recent research indicating that there are two different kinds of input from the reticular activating system to the hippocampus and neocortex. One input is probably cholinergic; it may play a role in stimulus control of behavior. The second input is noncholinergic and appears to be related to motor activity; movement-related input to the neocortex may be dependent on a trace amine.

Reticulo-cortical systems are not related to arousal in the traditional sense, but may play a role in the control of adaptive behavior by influencing the activity of the cerebral cortex, which in turn exerts control over subcortical circuits that co-ordinate muscle activity to produce behavior.