Colonization by Clostridioides difficile is common in children with inflammatory bowel disease (IBD) and complicates both the management of IBD and the diagnosis of C. difficile infection (CDI). There is a paucity of data on rates, risk factors, and outcomes associated with asymptomatic C. difficile colonization in children with IBD. We enrolled and prospectively followed 87 children with IBD without acute gastrointestinal symptoms. Twelve patients (13.8%) tested positive for C. difficile and were considered to have asymptomatic colonization. Elevated white blood cell count was associated with C. difficile colonization based on univariate regression. Three of the 12 (25%) C. difficile colonized patients were diagnosed with CDI in the 90 days following screening for C. difficile, versus 0 of the 75 who tested negative for C. difficile (p = 0.002). This data set the stage for further longitudinal tracking of children with IBD for C. difficile colonization and associated outcomes.