Brainstem

The brainstem includes the midbrain, pons, and medulla oblongata, and is structurally contiguous with the spinal cord. It connects the brain to the motor and sensory functions of the peripheral nervous system and plays an important role in the autonomic nervous system, including regulation of heart rate, respiratory function, consciousness, sleep/wake cycle, and digestion.

ME/CFS
A 1995 study found hypoperfusion (reduced blood flow) to the brainstem in patients with ME/CFS. In 2011, a study of brain involvement in CFS found "a strong correlation" brainstem gray matter volume and pulse pressure, "suggesting impaired cerebrovascular autoregulation."

A 2014 Japanese PET study looked at neuroinflammation in 9 patients with ME/CFS and 10 controls. They measured a protein expressed by activated microglia, and found that values in the cingulate cortex, hippocampus, amygdala, thalamus and parts of the brainstem, namely the midbrain, and pons, were 45%–199% higher in ME/CFS patients than in healthy controls. The values in the amygdala, thalamus, and midbrain positively correlated with cognitive impairment score, the values in the cingulate cortex and thalamus positively correlated with pain score, and the value in the hippocampus positively correlated with depression score.