Background: Discrimination of inflammatory bowel diseases (IBD) and other gastrointestinal diseases in pediatric patients is highly important and the definitive diagnosis of IBD is established by endoscopic examination. the use of noninvasive methods (clinical symptoms and laboratory tests) allows an early and accurate referral of patients from first step health centers to advanced health centers. In the present study, we aimed to investigate the effectiveness of fecal calprotectin (FC) in the discrimination of IBD and other gastrointestinal diseases in children. Methods: The retrospective study included the patients that underwent FC testing and colonoscopy. Demographic characteristics, Alarm symptoms (AS), and abnormal laboratory findings (ALF) were recorded for each patient. A negative calprotectin result was considered to be less than 50 μg/g, and a second cutoff value for FC was accepted as 150 µg/g. Definitive diagnosis was established by colonoscopy in each patient. Results: The study included 88 consecutive patients (mean age, 10.2 ± 6.1 years; 51.1% female). Of these, 20 (22.7%) patients were diagnosed with IBD. No significant difference was found between IBD and non-IBD patients with regard to AS except for involuntary weight loss (p=<0.001). The incidence of increased CRP and hypoalbuminemia was significantly higher in IBD patients (p=0.002 and p=0.026, respectively). AS combined with ALF and FC >150 µg/g had the highest specificity (95.12%). Conclusions: Although primary care clinicians often use AS and laboratory parameters in the discrimination of IBD and non-IBD diseases, FC was found to have a relatively higher diagnostic value.