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Pediatric inflammatory bowel disease (IBD) is in the differential diagnosis for children presenting with chronic diarrhea. During evaluation, stool studies are typically obtained to evaluate for an infectious source, and stool culture has been the conventional testing modality for bacterial pathogens. Recently, there has been increased utilization of molecular testing for enteric pathogens, including multiplex PCR. While these tests are highly sensitive for the detection of diverse pathogens, the clinical significance of positive results may not always be clear. We report two pediatric cases presenting with diarrhea and positive enteric pathogen (Biofire FilmArray GI Panel) PCR panels, but ultimately diagnosed with IBD. In one case, the PCR test results delayed diagnosis; in the other, they were ignored without any clinical consequence. In children with symptoms concerning for IBD, endoscopic evaluation should not be delayed based on positive molecular testing alone, especially when parallel culture for the same organism is negative.