ObjectiveRemote investigation and monitoring have gained importance in ambulatory practice. A home‐based fecal calprotectin (FC) test has been developed where the sample is processed and analyzed at home through a smartphone application. We aimed to assess the use of standard ELISA (sFC) versus home‐based (hFC) FC testing in a general pediatric gastroenterology clinic.MethodsAmbulatory pediatric patients with hFC or sFC performed between August 2019 and November 2020 were included. Data regarding demographics, clinical characteristics, medication use, investigations, and final diagnosis, categorized as inflammatory bowel disease (IBD), functional gastrointestinal (GI) disorders, organic non‐IBD (ONI) GI disorders, non‐GI disorders, and undetermined after 6 months of investigation, were recorded.ResultsA total of 453 FC tests from 453 unique patients were included. Of those, 249 (55%) were hFC. FC levels (median) were higher in children with IBD compared to non‐IBD diagnosis (sFC 795 vs. 57 μg/g, hFC 595 vs. 47 μg/g, p < 0.001), and in ONI compared to functional GI disorders (sFC 85 vs. 54 μg/g, p = 0.003, hFC 57 vs. 40 μg/g, p < 0.001). No significant difference was observed between different ONI GI disorders or subtypes of functional disorders. Age did not significantly influence levels.ConclusionsOverall, hFC and sFC provide similar results in the general pediatric GI ambulatory setting. FC is a sensitive but not disease‐specific marker to identify patients with IBD. Values appear to be higher in ONI GI disorders over functional disorders, although cut‐off values have yet to be determined.