Alertness and sleep are dependent on the activity of the brain as a whole, although different levels of consciousness are determined primarily by areas of the brain stem. A key anatomical structure in the regulation of waking and sleeping, (and thus consciousness), is the reticular formation, located in the brain stem. It is a highly complex interlacing network of fiber bundles. Neuro chemically, there is a great diversity of neurotransmitters present: serotonin, mainly from the mid-line raphe nuclei; noradrenaline from the locus coeruleus; acetylcholine from pedunculopontine nuclei with also peptidergic and dopaminergic components.

The alterations in the activity of these neurotransmitters either triggers or accompany the onset of natural sleep and distinguish slow wave or non-REM from REM sleep thus providing one of the most compelling arguments in favour of chemical neurotransmission being specifically involved in mechanisms of conscious awareness.

Pharmacological manipulations of these neurotransmitters provide evidence for the role of neuro chemical processes in consciousness. In this context it is important to understand that there are two categories of drugs used to vary the level of neurotransmitters.