Functional gastrointestinal disorders (FGIDs) affect millions of people without regard for age, race or sex, but little information related to FGIDs and few methods are available for diagnosing FGIDs. Therefore, the aims of this study were to investigate any alterations to the gastrointestinal tracts induced by FGIDs and to develop and test an ultrasonic diagnostic system capable of detecting the alteration in the gastrointestinal tract. Palpation/percussion examinations were performed on 40 participants with or without FGIDs to identify any mechanical alterations to the gastrointestinal tract induced by FGIDs. An ultrasonic diagnostic system for FGIDs was developed and clinical trials were performed on same participants used in the palpation/percussion examinations to test the system under actual clinical conditions. The results obtained from the palpation/percussion examinations showed that a gastrointestinal tract with a FGID became more rigid than a healthy tract (p < 0.05). Clinical trials also showed that gastrointestinal tracts in the patient group with FGIDs were in fact more rigid than those in the control group without FGIDs (p < 0.05). These findings indicated that our newly designed ultrasonic diagnostic system may be useful in clinics to accurately diagnose FGIDs through detecting mechanical alterations to the rigidity of the gastrointestinal tract induced by FGIDs. The current study may be valuable by identifying for the first time mechanical alterations of the gastrointestinal tract induced by FGIDs and may prove valuable as the first step in the development of a diagnostic system for FGIDs.