Functional gastrointestinal disorders have been related with different psychological conditions. On the contrary, the role of psychological factors within gastrointestinal motor disorders remains unclear. The objective of this study was to explore the differences and congruence with clinical performance of the psychological profile and subjective functionality among patients diagnosed with functional gastrointestinal disorders and gastrointestinal motor disorders. Using a double-blind design, 56 inpatients from a Gastroenterology Department were included in the study. No major differences were detected between the two groups. However, clinical performance was coherent with subjective physical functioning only among patients diagnosed with gastrointestinal motor disorders. These results may provide useful information for gastroenterologists dealing with patients’ complaints not consistent with their clinical profile.