BACKGROUND AND AIMS: Gastrointestinal pathogen panels (GPPs) are increasingly being used for evaluation of diarrhea. The impact of these tests on patients with inflammatory bowel diseases (IBD) is unknown. We performed a time-interrupted cohort study comparing GPPs and conventional stool evaluation in patients with IBD with diarrhea. METHODS: We included 268 consecutive patients with IBD who underwent GPP (BioFire Diagnostics) (n = 134) or conventional stool culture and Clostridium difficile polymerase chain reaction testing (n = 134) during suspected IBD flare between 2012 and 2016. Primary outcome was composite of 30-day IBD-related hospitalization, surgery, or emergency department visit; secondary outcome was IBD treatment modification. RESULTS: Overall, 41/134 (30.6%) patients tested positive on GPP (18 C. difficile, 17 other bacterial infections, and 6 viral pathogens) versus 14/134 patients (10.4%, all C. difficile) testing positive on conventional testing. Rate of IBD treatment modification in response to stool testing was lower in GPP group as compared conventional stool testing group (35.1 vs. 64.2%, p < 0.01). On multivariate analysis, diagnostic evaluation with GPP was associated with three times higher odds of IBD-related hospitalization/surgery/ED visit (95% CI, 1.27-7.14), as compared to conventional stool testing. This negative impact was partly mediated by differences in ordering provider specialty, with non-gastroenterologists more likely to order GPP as compared to gastroenterologists. CONCLUSIONS: In patients with suspected flare of IBD, GPPs have higher pathogen detection rate and lead to lower rate of IBD treatment modification. A diagnostic testing strategy based on GPPs is associated with higher hospital-related healthcare utilization as compared to conventional stool testing, particularly when utilized by non-gastroenterologists.