Dyspeptic symptoms may not allow clinicians to differentiate organic and functional gastrointestinal disorders. According to our dyspeptic patients' answers to dyspepsia questionnaire, we aimed to define the symptom scores directing organic dyspepsia (OD) before upper gastrointestinal endoscopy. One hundred sixty-one patients (ages 10-17 years, mean 13.5 ± 2.3 years, male/female: 2/3) with chronic upper gastrointestinal system symptoms lasting for at least 3 months were enrolled. Patients with predominated reflux symptoms were excluded by 24-hour pH monitoring. Before upper gastrointestinal endoscopy, severity and incidence of 8 gastrointestinal symptoms (epigastric pain, upper abdominal discomfort, retrosternal pyrosis, bitter or sour taste in mouth, halitosis, belching, nausea, and early satiety) were measured by 5-point Likert scale. Total score indicated severity score multiplied by incidence score. Antral biopsy samples were obtained. OD is defined as peptic ulcer, erosive esophagitis, erosive or nodular gastritis, and erosive duodenitis in endoscopy and/or moderate to severe antral gastritis in histology. Functional dyspepsia (FD) is defined as normal findings/mucosal hyperemia in endoscopy and/or mild antral gastritis in antral histology. We evaluated the relation among severity and incidence scores of each dyspeptic symptom in patients with OD or FD. Age, sex, body mass index, drug history, nutritional habits, the quality of life related to dyspepsia were also investigated in patients with OD and FD. According to patients' histological and endoscopic findings, 100 (62%) patients were in the OD group and 61 (38%) patients were in the FD group. Of the dyspeptic complaints, the severity, incidence, and total scores of epigastric pain were significantly correlated with dyspepsia type (respectively, P = 0.042, P = 0.028, and P = 0.005). Of 93 patients who had an epigastric pain severity of 4 and 5 (namely, moderate to severe pain), 65 (70%) patients were in the OD group and 28 (30%) patients were in the FD group. Of 68 patients who had an epigastric pain severity of 0 to 3 (no epigastric pain or mild pain), 33 (48.5%) were in the OD group and 35 (51.5%) were in the FD group, and the difference was statistically significant (P = 0.042). After analyzing the total scores of 8 dyspeptic symptoms, one by one or in different combinations, we could not find a threshold (cutoff) score value that was able to indicate OD definitely. Age, sex, body mass index, and nutritional habits were not significantly different between patients with OD or FD. Nocturnal abdominal pain, pain before meals, and resolution of symptoms after meals or ingestion of antacid drugs were not significantly related to OD. Nocturnal abdominal pain was observed to be higher in the group with moderate to severe gastric inflammation. In the present study, the severity, incidence, and total scores of epigastric pain were significantly related to OD; however, a cutoff value of dyspepsia symptom score for differentiation of OD and FD could not determined. In our study, Likert dyspepsia scale was not beneficial in differentiation of the OD/FD groups. We suggest that the Likert dyspepsia scale should be redesigned for children or the same scale should be applied in a larger cohort of dyspeptic children.