Background: Intestinal infections have been claimed to precipitate or aggravate flares of inflammatory bowel disease (IBD). The reported incidence of such infections among IBD patients varies between 9 and 13%, but only a few prospective studies have been conducted. Aims: To evaluate the incidence of intestinal infections by enteropathogens in patients with active IBD, their impact on clinical outcome, and to identify associated risk factors. Patients and Methods: Consecutive patients admitted because of a relapse or suspected onset of IBD were prospectively included. At admittance, stool samples for culture, examination for intestinal parasites, and cytotoxin assay for Clostridium difficile were collected. Baseline clinical characteristics, potential risk factors for gastrointestinal infections, and clinical outcome were recorded. Results: Ninety-nine episodes were included. Six intestinal infections were diagnosed in 6 patients (5 ulcerative colitis, 1 ileocolonic Crohn’s disease), Campylobacter jejuni being the most frequent isolated microbe (n = 5). None of the patients with intestinal infection needed surgery, but two of them required second-line therapies. Conclusions: Gastrointestinal infections among IBD patients do not exceed 10% and occur mostly in patients with extensive involvement of the colon. Infection by enteropathogenic bacteria does not appear to be associated with a poorer clinical outcome of the IBD flare.