Introduction: Chronic abdominal pain in children is mostly functional, but in association with alarm symptoms such as recurrent vomiting, it is necessary to determine proper tests for the diagnosis of probable underlying organic problems. Case Presentation: Four patients with chronic refractory abdominal pain and nonspecific gastrointestinal symptoms presented to our tertiary pediatric center. After thorough medical and psychological investigations and hepatobiliary scintigraphy, and calculating gallbladder ejection fraction, laparoscopic cholecystectomy was performed. One year after the surgery, they were relatively symptom-free and returned to their routine life. Conclusions: Biliary tract abnormalities should be considered as a probable cause of chronic abdominal pain in children. Hepatobiliary scintigraphy can provide promising results to help to identify the underlying causes of chronic abdominal pain in association with nonspecific gastrointestinal manifestations.