Background: Chronic abdominal pain in children is a common disorder. For an accurate diagnosis of its cause, sometimes invasive diagnostic procedures such as endoscopy should be performed. Objectives: The purpose of the study was to evaluate the fecal calprotectin in children with upper gastrointestinal signs and symptoms and to compare it with endoscopic findings. Methods: A total of 131 children aged 1-14 years with upper gastrointestinal symptoms were enrolled during 2012 -2013 at two centers. One hundred and twenty patients underwent endoscopy and biopsy. Before endoscopy, the level of calprotectin was measured by the enzyme-linked immunosorbent assay test in stool samples and the results were compared with the endoscopic and pathology findings. Results: Of the 120 children included in this study, 71 (59.2%) were males and 49 (40.8%) females with a mean age of 93.6 months. Of the 112 patients in whom biopsies were taken, 16 had esophagitis, 89 chronic gastritis (79.5%) and 57 colonization with Helicobacter pylori. Conclusions: There was a statistically significant correlation between fecal calprotectin and gastritis and severity of H. pylori infection. Fecal calprotectin level measurement can avoid unnecessary endoscopies and is also useful for evaluation of therapy response.