The brain stem consists of the mesencephalon, pons, and medulla oblongata and contains the nuclei of the cranial nerves III to XII, their complex connectivity, the ascending and descending fibre tracts, and the cerebellar connections. The corticobulbar and corticospinal tracts and the medial lemniscus cross its midline. Vital functions such as wakefulness, respiration, swallowing, and circulation are controlled there. Here we discuss acute brain stem syndromes of vascular, inflammatory, and toxic-metabolic origin. They present frequently with alternating symptoms, i.e. ipsilateral cranial nerve deficits associated with contralateral signs of long-fibre tract involvement and with various disturbances of the oculomotor system. Modern diagnostic and therapeutic approaches are described along with clinical presentation.