Brainstem encephalitis represents around 20% of all cases of encephalitis and has unique clinical and epidemiological features. The best-characterized brainstem encephalitis include opsoclonus-myoclonus syndrome (OMS), Bickerstaff encephalitis, paraneoplastic brainstem encephalitis, and chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (CLIPPERS). The main causes of OMS are paraneoplastic, post-infectious, and idiopathic; it is likely that they share an immune-mediated pathophysiology, although neuronal antibodies only occur in a subgroup of patients with OMS and breast cancer who develop Ri antibodies. Other paraneoplastic brainstem encephalitis can associate with Ma2 and Hu antibodies. Patients with Bickerstaff encephalitis frequently develop overlapping features with Miller–Fisher syndrome (characterized by bilateral ophthalmoplegia, ataxia, and areflexia). The identification of GQ1b antibodies in both disorders suggests that they are part of the same spectrum of disease that has been designated anti-GQ1b syndrome. The diagnosis of CLIPPERS is mainly based on the presence of suggestive brain MRI abnormalities. However, similar MRI lesions can occur in systemic autoimmune diseases that may affect the brainstem, particularly Behçet disease or sarcoidosis, and in primary lymphoma of the central nervous system. CLIPPERS does not have a specific biological marker.