Objectives Previous research on gastrointestinal and other medical conditions has shown the presence of incongruence between self- and clinician-reported functioning and its relation with psychopathology. The main objective of this study was to test whether inconsistencies between clinician- and self-assessed functionality can be used to detect psychopathology among patients diagnosed of motor or functional gastrointestinal disorders. Methods One hundred and three patients from a gastroenterology inpatient unit were included in this study. All patients underwent clinical assessment, including intestinal manometry, Rome III criteria for functional gastrointestinal disorders, and psychological and psychiatric evaluation. Patients with suspected gastroparesis underwent a scintigraphic gastric emptying test. Definitive diagnoses were made at discharge. Results Patients with higher levels of incongruence differed in various sociodemographic (age, educational level, work activity and having children) and psychopathological (all SCL-90-R subscales except anxiety and hostility) characteristics. Using general lineal models, incongruence was found to be the variable with stronger relations with psychopathology even when controlling for diagnosis. Interactions were found between incongruence and diagnosis reflecting a pattern in which patients with functional disorders whose subjective evaluation of functioning is not congruent with that of the clinician, have higher levels of psychopathology than patients with motor disorders. Conclusions Incongruence between clinician and self-reported functionality seems to be related to higher levels of psychopathology in patients with functional disorders. These findings underscore the need for routine psychosocial assessment among these patients. Gastroenterologists could use the concept of incongruence and its clinical implications, as a screening tool for psychopathology, facilitating consultation-liaison processes.