Aim: The differentiation of inflammatory bowel diseases (IBD) from other gastrointestinal diseases in pediatric patients is highly important and the definitive diagnosis of IBD is established by endoscopic examination. The use of non-invasive methods (clinical symptoms and laboratory tests) allows for the early and accurate referral of patients from first step health centers to advanced health centers. We aimed to investigate the effectiveness of fecal calprotectin (FC) in the differentiation of IBD from other gastrointestinal diseases in children. Materials and Methods: This retrospective study included patients who had undergone FC testing and colonoscopy. The 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 cut-off 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 the presence of AS except for involuntary weight loss (p<0.001). The prevalence of increased C-reactive protein and hypoalbuminemia was significantly higher in the IBD patients (p=0.002 and p=0.026, respectively). FC>50 μg/g [80.0 vs 39.7%, p=0.044, odds ratio (OR): 6.07, 95% confidence interval (CI) 1.83 to 23.42] and >150 μg/g (60.0 vs 16.2%, p=0.002, OR: 7.78, 95% CI 1.83 to 20.14) was significantly higher in the IBD patients compared to the non-IBD patients. AS combined with ALF and FC>150 μg/g had the highest specificity (95.12%). Conclusion: Although primary care clinicians often use AS and laboratory parameters in the differentiation of IBD from non-IBD diseases, FC was found to have a relatively higher diagnostic value.