Despite significant advances in the recognition of etiological factors and pathological mechanisms, the pathophysiology of functional gastrointestinal disorders (FGD) is still not fully understood. Visceral hypersensitivity has been recognized as a characteristic of patients with FGD, especially in patients with irritable bowel syndrome (IBS). Visceral afferent input is modulated by a variety of mechanisms, operating between the gastrointestinal tract and the brain. Dysfunction of these regulatory mechanisms could distort gastrointestinal perceptions. Recent findings suggest that in the majority of cases of IBS the primary abnormality may be at the periphery with alterations of the motor and secretory sensory activity. Although imaging techniques indicate that there are also differences in cortical activation. Furthermore, selective serotonin reuptake inhibitors may benefit FGD. Recent pharmacological studies suggest that 5-HT3 antagonist such as alosetron and cilansetron, and 5-HT4 agonist such as legaserod and prucalopride may also have a potential use in FGD.