Clostridium difficile is an emerging opportunistic pathogen that infects patients with underlying chronic disorders such as inflammatory bowel diseases (IBD) at high rates. An extremely high prevalence of Clostridium difficile infection (CDI) was noted recently in new-onset pediatric IBD from eastern Europe (Poland). We examined the rate of CDI in our new pediatric IBD patients (123 tested) from 2010 to 2012. The overall prevalence of CDI at disease onset was 8.1%, significantly (P < 0.0001) lower than in Poland, but much higher than in the general population. This work supports the testing for Clostridium difficile in suspected cases of new-onset pediatric IBD.