Aims: The aim of this study was to determine the incidence of Clostridium difficile infection in hospitalized children with inflammatory bowel disease (IBD) and to compare it to other immunosuppressed patients at risk (oncology patients) as well as to immunocompetent patients. Methods: We analyzed data from all hospitalized children who underwent stool detection of C. difficile toxins A and B (n = 757) in a 5.5-year study period. Results: The number of positive tests was significantly increased in the oncology group compared to the IBD group (12.45 vs. 6.02%, p = 0.03) and immunocompetent group (12.45 vs. 5.7%, p = 0.01). Patients who had C. difficile infection used antibiotics prior to the test more often than patients who did not (12.69 vs. 1.73%, p = 0.03). Pearson’s correlation was positive for C. difficile infection and both antibiotics and immunosuppressants, while no correlation was found regarding age and gender. There were no significant differences regarding either IBD diagnosis (Crohn’s disease vs. ulcerative colitis, p = 0.71) or treatment used for IBD (p = 0.53) and C. difficile infection. Conclusion: In our setting, the incidence of C. difficile infection among hospitalized children with active IBD was found to be low. Children at increased risk for C. difficile infection were oncology patients receiving immunosuppressants and antibiotics.