Multiplex polymerase chain reaction based stool assays for gastrointestinal pathogens (GI PCR) allow for the timely and accurate detection of enteric infections that were poorly characterized by conventional means such as stool culture. Despite the increasing availability of these molecular diagnostic tools, few studies have evaluated their use in outpatients with inflammatory bowel disease (IBD). Our objective was to evaluate the burden and impact of enteric infections detected by multiplex PCR stool testing in outpatients presenting with flares of IBD.