A representative cohort of Swiss adults recruited at age 20 years and interviewed at ages 23, 28 and 30 years was studied regarding the symptomatology, prevalence and longitudinal course of functional gastrointestinal symptoms and their association with psychiatric syndromes. A functional gastrointestinal complaint was identified if a proband reported symptoms at least eight times in the past year or for a duration of at least 2 weeks without medical explanation and with a moderate degree of distress. Of the population, 9.4-17.7% was found to suffer from functional stomach complaints and 4.9-16% from functional intestinal complaints. Women reported functional gastrointestinal complaints two to three times more often than men, and increasingly so with age. The overlap of stomach and intestinal complaints was modest with 2.0-6.7%. Cross sectionally, functional stomach complaints were significantly associated with major depression (DSM-III-R), recurrent brief depression (RBD), subthreshold RBD and dysthymia, and with subthreshold panic disorder, agoraphobia, social phobia and recurrent brief anxiety. Functional intestinal complaints showed a consistently significant association with RBD, dysthymia, major depression, subthreshold RBD, panic disorder, subthreshold panic disorder, agoraphobia, simple and social phobia and generalized anxiety disorder. Individuals who at younger ages suffered from functional gastrointestinal complaints did not show an increased risk for a subsequent development of an anxiety or depressive disorder. Functional gastrointestinal complaints reflect an unspecific concomitant vegetative disturbance common to depression and anxiety; they do not reflect a risk factor for the development of a specific anxiety or depressive disorder.