The objective of the present investigation was to evaluate the factor structure of the Children’s Depression Inventory (CDI) in adolescents with inflammatory bowel disease (IBD) in order to better understand the CDI’s psychometric properties in a medically complicated population. An exploratory factor analysis (EFA) was performed on CDI data collected from a clinical sample of 191 youth with IBD, aged 11 to 17 years. EFA with quartimax rotation yielded 3 factors: Mood, Behavioral/Motivational, and Somatic Complaints. Only the Somatic factor (i.e., fatigue, sleep, decreased appetite, worry about aches and pain) showed a significant positive correlation with IBD severity. The CDI holds promise as a brief measure for the assessment of depressive features psychometrically independent of IBD severity and common steroid treatments, as well as of non-gastrointestinal specific somatic complaints in a sample of adolescents with IBD. Continued work in this area of research appears promising in honing the assessment of depressive and somatic symptoms in youths with IBD.