Functional gastrointestinal (GI) disorders are common in the general population. Based on the Rome III classification, these disorders are mutually exclusive disorders keeping the homogeneity of each functional GI disorder in research area. In contrast, many population and clinical studies have reported a considerably high rate of overlap between functional GI disorders. The overlap of functional GI disorders over other intestinal diseases might simply occur by chance due to a highly prevalent disorder. Moreover, functional GI disorders is considered a chronic stable disorder that may wax and wane for several years. However, a recent study about the natural history of functional GI disorders showed substantial transition among functional GI disorders over time. The natural history of functional GI disorders with overlapping other functional GI disorders are still in infancy and better understanding of these will be important in determining the efficacy of future therapeutic interventions.