Although functional gastrointestinal disorders (FGID) are common, their pathophysiology remains incompletely understood. It is generally accepted that dysfunction of the bidirectional pathways between the gastrointestinal tract and the central nervous system (the 'brain-gut axis') at any level can cause FGID symptoms. In this review article, we focus on the role of the central nervous system in the brain-gut axis. First, we describe the functional anatomy of the brain-gut axis. Second, we focus on the results from brain-imaging studies both in healthy volunteers and in FGID patients. These new investigational techniques made identification of brain regions critically involved in processing of visceral afferent information possible. Differences in central nervous system response to visceral stimuli between controls and FGID patients will be highlighted. Third, we will address the issue of high comorbidity with psychiatric disorders. Some hypotheses about common pathophysiological substrates will be discussed.