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The brainstem is one of the least understood parts of the human brain despite its prime importance for the maintenance of basic vital functions. Owing to its role as a relay station between spinal cord, cerebellum and neocortex, the brainstem contains vital nodes of virtually all functional systems in the central nervous system and, thus, is a crucial structure to study. Among many others, it contains sensory, motor, autonomic, neuromodulatory and cranial nerve nuclei. While the brainstem has been extensively studied in animals using invasive methods, human studies remain scarce. This is unfortunate, since the brainstem is a major target in many neurodegenerative diseases, like Parkinson's disease, multiple system atrophy and spinocerebellar ataxia, whose pathophysiologies are poorly understood. Others, like stroke, multiple sclerosis and encephalitis also frequently affect the brainstem and even small lesions may cause severe long term neurological deficits. Hence, a better understanding of human brainstem structure and function is a prerequisite for developing novel targeted therapeutic strategies for the treatment of such disorders. Magnetic resonance imaging (MRI) as a non-invasive and widely available method is one possibility to access the brainstem in humans and measure its structure as well as function. The close vicinity of the brainstem to large arteries and ventricles and the small size of the anatomical structures, however, place high demands on imaging as well as data analysis methods. Nevertheless, the last years have seen some important advances in, both, structural and functional MRI of the brainstem. It is the goal of this research topic to compile the state of the art in functional and structural MRI of the human brainstem in health and disease and to bring together those scientists working in the field. Researchers either engaged with methodological developments of human brainstem MRI, atlas development, or clinical applications are cordially invited to contribute to this special issue. Hosted by: Florian Beissner, Simon Baudrexel Deadline for abstract submission: 01 Mar 2013 Deadline for full article submission: 01 May 2013 website: http://www.frontiersin.org/human_neuroscience/researchtopics/Investigating_the_human_brains/1196