Background & Aims: Clostridium difficile infection (CDI) and colonization is a common complication in inflammatory bowel disease (IBD) and is associated with poor outcome. The aims of our study were to evaluate the incidence of CDI and colonization in pediatric IBD patients at diagnosis and to find out risk factors of CDI in pediatric patients during the course of IBD treatment. Method: We recruited pediatric IBD patients (n = 59) and the age- and sex-matched controls (n = 59) from pediatric IBD database of our tertiary medical center between March 2011 and June 2017. Demographic and clinical data were reviewed retrospectively. All study subjects underwent the tests for toxin assay and culture for Clostridium difficile. Kaplan-Meier survival analysis and Cox regression test were used for the analysis of risk factors during treatment. Results: Initial culture was positive for Clostridium difficile in 13 patients (22%) of the IBD group and 2 (3.4%) of the control group, whereas Clostridium difficile toxin assay were positive only in 3 patients (5.1%) of the IBD group at initial diagnosis and none (0%) of the controls. During IBD treatment, Clostridium difficile cultures converted to positive in 28 (60.8%) patients in addition to 13 patients who were initially culture-positive, and Clostridium difficile toxins converted to positive in 13 (23.2%) patients in addition to 3 patients who were initially toxin-positive. Out of demographic and clinical factors, only the administration of antibiotics was significantly associated with fecal conversion to Clostridium difficile colonization (p =.011), and only the duration of admission was associated with conversion to CDI (p = .032). Conclusion: Clostridium difficile colonization and CDI occurs frequently during the disease course of pediatric IBD patients on treatment. Our study revealed that only antibiotics usage and longer hospital stay were significant risks factors for the conversion of Clostridium difficile status in pediatric IBD patients during IBD treatment.